This question is asked by a number of Mefarshim:

1) The Gemara here (end of 60b) cites the Beraisa in which Rebbi Yishmael ben Elisha says that ever since the wicked kingdom passed decrees to annul the Torah and Mitzvos, the Din should really be that we make a decree on ourselves not to marry and bear children.

How does this reconcile with the Gemara in Sotah 12a where we learn that Amram, who was the greatest in his generation, divorced his wife when Pharaoh said that all the sons should be thrown into the river? Everyone else followed his example and divorced their wives. Miriam said to her father Amram that his decree is worse than Pharaoh's, because Pharaoh's decree was only against the male children while Amram's decree was against the female children also.

Amram changed his mind and took his wife back, and everyone else followed him and remarried their wives.

The question is, since Amram agreed to his daughter that it is better to raise a family even though we do not know if the children will be able to live according to the Mitzvos of the Torah, why did the Beis Din in the time of Rebbi Yishmael ben Elisha not learn from Amram's conclusion? Why did they say that according to the Din we should make a decree not to marry?

2) I can suggest an answer according to what I saw in the Hagadah Shel Pesach "Si'ach Yitzchak," based on the Gemara in Berachos 10a. Chizkiyah ha'Melech saw that he would have unworthy sons, so he did not marry. Yeshayahu ha'Navi chastised him for this. He said that Chizkiyah should not pay attention to hidden matters which only Hash-m understands properly. Instead, Chizkiyah must fulfil the Mitzvos of the Torah without trying to figure out what will be their end result. He should perform the Mitzvah of being fruitful and multiplying. Chizkiyah did not know that the righteous king Yoshiyahu would be from his descendants. A similar thing happened to Bnei Yisrael in Egypt. They thought they were in a very lowly state and nothing good would come of them, but Hash-m knew that they would attain a great level of prophesy -- such that even a simple maidservant would see at the Splitting of the Sea what Yechezkel ha'Navi did not merit to see.

We can say that when Rebbi Yishmael ben Elisha here says that according to the "Din" we should make a decree not to marry, this does not mean that the Beis Din actually tried to make a decree, or even thought of doing so. Rather, the word "Din" means "according to logic." According to human logic, there is no point in having children in such a situation. But the Halachah does not always follow people's logic. Rather, we have to carry out the Mitzvos of the Torah and Hash-m will see to it that things work out in the best possible way for us.

3) However, there is a problem with the above answer -- namely, that the decree of Rebbi Yishmael is cited by the practical Halachic authorities. The earliest source that I know for this is one of the Rishonim, the Mordechai (Yevamos #50, printed in the back of the Gemara after the Rif). The issue is: if a couple have been married for ten years and are not able to have children, do we obligate them to divorce so that the husband can take a different wife and fulfill the Mitzvah of having children? One of the sources that the Mordechai cites as support that we do not obligate them to divorce is our Gemara. He writes that since the Gemara says that we should really make a decree not to marry, at the very least we should not force a couple to divorce in such a case.

In addition, the Mordechai is cited by the Beis Shmuel on the page of the Shulchan Aruch (Even ha'Ezer 1:6). Referring to what the Shulchan Aruch (1:3) writes that if a man does not want to get married, the Beis Din forces him to do so, the Rema writes that nowadays the custom is not to force anyone on this. The Beis Shmuel (#6) cites the Mordechai in the name of our Gemara as a source for this Halachah, that really Chazal should have made a Gezeirah not to marry at all, so at least we do not force people to marry. For the same reason, if a man who does not yet have children wants to marry a woman incapable of having children, or if a couple have been married for ten years without children, the Beis Din do not intervene.

This all contradicts what I wrote above, that the Beis Din in the time of Rebbi Yishmael ben Elisha never actually thought of making a decree against marriage. Rather, the Mordechai understands our Gemara literally, that Chazal would really have wanted to make such a Gezeirah but the people could not live with such a Halachah.

4) I suggest a different answer to the original question. The difference between Miriam and Rebbi Yishmael ben Elisha is what Miriam herself said, that Pharaoh did not make a decree on the girls. If Pharaoh would have said that the girls should also be killed, then Miriam would have agreed to everyone divorcing his wife (at least everyone who already had a boy and girl, as Tosfos here (DH Din) writes), but since the girls were not in danger Miriam said that they should at least be born. But she would have agreed to Rebbi Yishmael ben Elisha's idea of making a Gezeirah in his times, since neither boys or girls would be able to keep the Mitzvos.

5) I later saw a clear answer to this question in the Sefer "Ha'er Eineinu" on Bava Basra, by Rav Eliezer Roth shlit'a (son-in-law of Rav Yitzchak Zilberstein shlit'a). He sees this answer in the words of the Rashbam (DH v'Nimtza) who writes that the seed of Avraham will cease "in a good way, and not through Akum, and Mitzvos will not be annulled anymore."

The crucial point is that "Mitzvos will not be annulled anymore." This was the difference between the decree of Pharaoh and the decree of the Romans. Pharaoh did not make a decree against Mitzvos; he made a decree on the bodies of the male children. The decree of the Romans was worse. They decreed that the Jews should live without Mitzvos. To live without Mitzvos is worse than dying. Therefore, Miriam said that all the couples should remarry. The Egyptians might later on kill the boys but those still alive can still observe the Mitzvos. In the time of Rebbi Yishmael it was worse. The Mitzvos might be annuled, so it was worth making a Gezeirah to prevent the violation of Mitzvos.

Kol Tuv,

Dovid Bloom