About Kira Nerys

[Mage]

Except they were actually trained to serve on starships unlike Kira.

Sure she was. We just never saw it on screen. But because we never saw it, people will say non-canon.
And yes, now people will say a short throw-away line on Dax asking her how her training was going would have been enough. Well, they didn't think of that. Just imagine that Kira got training in between episodes and everything works out fine.

 

[Sci]

I've got an even better explanation.

After Sisko convinced the Prophets to do whatever they did to the 2,800 Dominion ships, the Bajorans decided to throw the non-aggression pact in the waste extraction system and side with the Federation.

Something as major as what happened there was certainly a bigger convincing statement than a Federation/Klingon fleet always being at DS9. At least, to the Bajorans.

Excellent point -- the role of the Prophets may definitely have played a role in persuading the Bajoran government to formally ally with the Federation and Klingons.

 

[FederationHistorian]

Although she was Sisko's first officer on DS9, what qualification did she have to take command of the Defiant in his absence and what authority did she have to give orders to Starfleet personal like a Starfleet officer?

The Defiant as an auxiliary of DS9 is to protect and defend Bajoran space, and other Federation interests.

Kira, being the Bajoran liaison and Sisko’s first officer, would be qualified to take the Defiant out in the name of defending Bajor.

ow did she know about Starfleet battle strategies when the Defiant was in combat

She probably practiced offscreen in the holosuite.

why was she written to act like and be treated like a Starfleet officer despite previously being part of a rebel militia?

Ignoring the real world reasonings being that Kira was originally intended to be Ro Laren...

Kira behaved like a Starfleet officer for the same reason the Maquis behaved like Starfleet officers on Voyager: it was in her best interest to do so.