Actually that makes the Federation's involvement in this make even more sense then. Not only will this get us great medical technology which will save lives for the war, but it takes a potential ally away from the Dominion.
Your OP did speculate they were "allies" though, not partners AllStarEnterprise, hence my original reaction though. As for trading with the neutral S'ona? That actually makes perfect sense. They're neutral and the Federation isn't about to start the equivalent of unrestricted submarine warfare, and it's stated a few times in Season 6 that white supplies were getting low, so having a neutral power make it that's not going to be targeted makes a good amount of sense.