Funny cause I had more trouble with stains when dd was ebf. I haven't seen a stain in many, many moons. I'm like you OP, stains bug me- I feel like it's not really cleaned off of there if it's stained. We toilet dunk our poopie dipes and sometimes leave them sitting in there for a few. The cold water really gets stains out. Then I squirt them with a little bac-out before tossing in pail. Additionally, I do a cold wash cycle before my hot wash (fl washer) to rinse everything. Some people do a cold soak in their washer. And, since dd LOVES blueberries more than just about anything, we've had more than our share of blueberry bombs. And I mean BOMB. But no stains that I can see at present. If you don't like dunking, do you have a diaper sprayer?
A little bleach every now and then will not immediately "mess up" your dipes, although it's harder on pul. Bleach wears any fabric out faster, so the more you use it the shorter the fabric lifespan. I rarely use it in any of my laundry unless absolutely necessary because it's not very environmentally friendly and it's hard for me to get it rinsed out thoroughly, and I'm overly sensitive to it. But if you just used a little on the rare occasion and rinsed it thoroughly, there shouldn't be any problem. Me, I prefer to try other techniques, like more cold water, before bleach- unless we had like a staph outbreak or something serious like that.