It does seem like this is hardest to do in the early game, where combats don't get tedious, and becomes easier later on, so at least the structure of it nicely dovetails with that. It seems from my own playthrough though that earning credits in the late game is still best done by going to some homeworld with massive defense fleets and just running through dozens of attacks on their armada; the x3 multiplier means you can get ~4k credits per fight, which basically trumps almost every other option I've found to earn credits. When you're trying to build up 50k to ask the Skylaxians to get someone into the Federation, it can seem like this sort of grinding is basically what you should be doing, but it doesn't really make logical sense. It also means that you can raise very large amounts of credits over the course of a short time, given some conflict like that to meddle in, which may or may not be a good thing for strategic depth.
I think honestly autoresolve doesn't mesh with the way the game is currently working, especially with Permadeath from fights disabled by default. Rather, its probably best to just increase the degree to which you can actually accomplish things without personally doing all the fighting - that means more non-combat ways to score reasonable credit income, non-combat ways to influence enemy fleets, etc.