Hmm, considering that management pushed to gain the studio's independence last year I doubt that the thought of an acquisition would cross their minds ...
If I remember correctly, the "divorce" was initiated by Square Enix and IO Interactive was searching a buyer at first until they done the management buyout. Perhaps they aren't 100% happy with the current situation where they ain't totally independant anyways (they still need the help of Warner Interactive for publishing) but take most of the risk.
If the offer of Microsoft is good, they'll probably take it and focus on development.
Brian Fargo wasn't a big fan of ubiquitous publishers either in the last decade and was proud of inXile's independence... just look at his Kickstarter promotion videos or FIG. That didn't stop inXile to join Microsft Studios.