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.
As for what happened with inXile and Brian Fargo, that was a decade ago like you pointed out. We don't know exactly what happened over the years that specifically changed his mindset or position on the matter given that views can change especially over such a long time frame ... Pretty sure Warner Bros is only there to handle the distribution just like they did for CD Projekt RED on the Witcher 3 so IO Interactive is practically independent ...
My understanding is that Hitman 2 is performing badly in sales. Probably they have no choice.
Seems like MS is buying a bunch of failing companies (who make good games).
Good for MS and the company. But do they have the management in place for so many teams so quickly?
Well on the bright side if they do acquire IO they can at least keep the series alive and seriously improve the engine technology along with it ...