Better to put it in and reduce flow than not and wish you had.
Are the tree roots the problem, or is the tree's location in regards to your layout the problem. If you worked for me and you didn't want to dig through the roots, well I'd hand you a saw and tell you lunch will happen when the head is in. If the tree is an obstruction that blocks a sprinkler, than a different layout is needed. Evenly spaced heads will give you what you want.
A diagram of your yard would be mighty helpful.
Thanks! The tree and roots are in the way. We have 4 large oak trees right by the lawn. I don't want to kill the trees, as the roots are the main ones for the tree (about 3"-5" thick!) Cutting them would risk the tree. The tree's themselves are also "in the way". But I solved that when I shifted the layout. I have gotten by a few roots before, either cutting them, or going under them....
Below is a image of the lawns. Front/back. The red dots are sprinklers I have in now. The boxes are the watering area needed. The dimensions are estimated from google earth's measurement tool, so it may be off a bit. You can see the trees in the front.