That the Female Founder agreed to stand trial to the deeds of the Dominion in the first place was probably due to the fact that she was being held at gunpoint, and she and Odo were the only ones in the universe with the means and goodwill to cure the Link. Had she not cooperated, the Link would probably have perished.
However, her reasons for cooperating would end once Odo went and cured the Link. The Alpha militaries would pose little threat to the Dominion as such - all the difficulty the Dominion had with conquering Alpha would essentially be reversed on the Alphans if they tried anything nasty.
At the end of "What You Leave Behind", the status and content of the ceasefire or peace treaty or whatever remains unknown. Nothing directly suggests Dominion disarmament or withdrawal from Cardassia, and there's very little to suggest that the Female Founder would have agreed to be jailed, either. One would think the Dominion would insist on the Female Founder's freedom no matter how the trial turned out, and would simply restart the war if the Alphans didn't comply. Then again, the Dominion might like to have a few decades to recuperate, and those decades would matter very little to the Female Founder. Perhaps she'd actually cherish the opportunity to intermingle with Solids (even if they are just her prison guards) and gather further psy-intel on the Alphans.
Timo Saloniemi
