You're not thinking big picture here. The resolution debate between PS4 and Xbox One has been percolating since the consoles launched, with an underlying and potentially damaging theme for Microsoft: the PS4 is more powerful and delivers superior third party games.
If Microsoft did strike up a deal, or otherwise offer Ubisoft some incentive toward parity, it would have been in an effort to curb this trend going forward, and this likely wouldn't have been the only instance of it occurring.
They wouldn't be considering the minuscule number of gamers that have a PS4 and Xbox One today or that would be purchasing a PS4 solely for AC:U. They'd be making a concerted effort, of likely many, to abate a constant trend of appearing less powerful in order to persuade purchasers for the future and buck the current stigma against the Xbox One.
This is why it's vital for gamers to speak up now, hell, even if Microsoft legitimately had nothing to do with it, to ensure these companies understand that consumers won't tolerate even a whiff of such anti-consumer practice.