1)
Who are "the Yehudim who were with [Gedalyah]"?
1.
Malbim: Those who were there for his need - to fight for him.
2)
Who are "Ba'alei ha'Milchamah"?
1.
Malbim: All the Bavliyim were Ba'alei ha'Milchamah. Therefore it says "Asher Nimtze'u Sham." From the Yehudim he struck only Ba'alei ha'Milchamah, and left the rest of the nation alive.