Sisko. Kira is out of control in the first few episodes.
If your first officer is seriously contemplating betraying Starfleet to join an anti-Federation terrorist group, and you kinda know about it, and continue to leave her in command of all your personnel and equipment, you might be a lenient captain.
^ I don't see it as that at all. Sisko even says to Kira in "Past Prologue" "Go over my head again and I'll have yours on a platter
Yes, he dealt with her insubordination, which is a separate problem. What concerns me more is the problem of her lack of loyalty to both her own government and to Starfleet, combined with experience that makes her capable of actually doing something about it.
He tries to talk to her about it, but he doesn't change her mind. Odo is the one who eventually gives her a push toward making the right decision.
Sisko was in an interesting position, though. Starfleet was there at the request of the Bajoran Provisional Government, for which Kira was an official representative. Yeah, it was risky in terms of lives and property for Starfleet and Sisko to keep her in place, but it would've been very risky for the mission overall to take such a hard-line, paternalistic approach as to remove her. I think Sisko was looking at the long game, and saw three scenarios:
1) he does nothing, Kira chooses loyalty, and their relationship is strengthened (or at least, not damaged).
2) he removes Kira from command, Kira chooses Tahna (possibly in retaliation for Sisko's acts), and his mission at Bajor is jeopardized as a result
3) he does nothing, Kira chooses Tahna and his mission at Bajor is jeopardized as a result.
It seems to me that Sisko was generally very mindful of problems that he couldn't solve through his own authority, and knew that this was one of them.