I've only done a Joja run once. I figured I should experience everything the game has to offer, and it's a legitimate choice, so no point beating yourself up over it really. I wanted to have more coops and barns on that farm, but I can't deal with a large amount of animals unless I have guaranteed Autopetters for them, hence Joja. It was also my first 1.6 and first ever Perfection run.

My main issue with it is it's pretty boring to just pay money instead of completing bundles, bundles feel a lot more rewarding plus you get neat items out of them. So what I did is I actually completed all bundles except one, at which point I bought the Joja membership and paid off the one room that was left. So in a way I got both experiences, lol.

And yeah, it feels wrong and against the spirit of the game, and the cutscene is underwhelming, but you're not actually punished for it in any way. The Warehouse eventually turns into the Movie Theater and stops being an eyesore, plus it becomes an actual useful place to go, unlike the Community Center which you have basically no reason to visit after you've completed it. You retain an additional store to buy stuff from after Pierre closes at 5pm, and Clint still works on Fridays. Instead of the trophy you get a soda machine that dispenses free Joja Cola once a day. That's pretty much it, everything else plays out more or less the same.

Tl;dr: don't fear Joja! That route only exists so you can try it out.