It will probably be fine. I would say you harvested rather than pruned. I hope you ate what you cut off. On the other hand, if you weren't sure what made you do it?

As long as it's getting enough light, you should be fine. You probably did go a little too far and it may slow the growth, but shouldn't kill it. With my seedlings, I usually start pinching after 4-5 pair true leaves, then down to the second or third set. It is best to count by leaf growth, rather than by height--a leggy seedling can be 5" tall with only one set of leaves.