They actually recommend that you pinch back Marigolds to allow for a more bushy growth habbit. Zinnias can also be pinched back, so by all means, go for it! chances are, the plants will all say THANK YOU!!

BTW, just how far are the lights back? And how much distance are you trying to keep between the lighting and the plants?

I keep the lights about an inch or two above the plants, which doesnt seem to matter since in a few days the plants grow so fast that they are touching the lights. I have roughly 2 feet between the shelves, and 4 shelves all together. The plants are in pots and the light fixture is almost to the bottom now of the shelf above it. I may very well have to pinch back each plant as some seem to be too leggy anyway.

It will be to their benifit to pinch them back. Go ahead!