what is it... ? a 2 inch net pot? leave the clone in it, who cares.
what type of system are you running? what are the details?
You can take that 2 inch netpot and throw it into a 3 inch or 5 inch netpot, OR, you could throw it in soil, I dont really see how it matters one way or the other.the roots will be fine, and they will find a way. I have a tree that's roots are lifting and cracking my garage foundation in half, I dont think a puny netpot is going to discourage roots from getting bigger or branching out.