I wouldn't worry about the small root system, tomatoes will root from the stem. I usually plant mine pretty deeply when I set them out in the garden. But I wouldn't plant too deeply at this stage I guess so they don't get damping off. At any rate, I never had trouble with tomatoes because of small root systems...they always seem to manage just fine.
Dropped to 18F last night so it will be A WHILE before I'm planting tomatoes here!