Go on, right now, go prune your peppers! The NEED it! Do you want little dainty plants or do you want them to go big?
If you want large plants and a lot of fruit then they need to be pruned. Peppers will start fruiting at the first sign of stress, but they will also start shooting their roots and digging in.
When transplanting that is naturally a stressful event so they may wilt a bit then start fruiting. the best thing you can to for them, at such an early stage, would be to prune them.
Aggressively top all of the branches and cut out all of the flower growth. I do this every couple of weeks until summer.
This method helps strengthen the plant and allows for more fruit to be grown. I know it can feel scary but in the end you will be glad you did!
**all pictures were taken by my wife