From a practical point of view, that probably sounds like a good idea. I played the
hell out of Incursion, and while there was a ton of neat things going on with it on the alignment front, it was a constant source of bugs, odd behavior, and general nuisance. If you're going to do it particularly well or dynamic (and
not regularly infuriate your playerbase) you're going to be adding a metric ton of complexity and coding interactions for relatively little gain. If you can go with a more simple system and save your efforts for other interesting, less finicky, AI et al interactions, it's probably a good idea.
... or in other words, if you're thinking about it leave some design space for future implementation and mess with it after you're done with basically everything
else, lest you spend the remainder of your development cycle(s) constantly beating your head against the alignment wall to get it to function decently