I've tried this quite a few times, and as long as you wash the dirt off and put it moist media within a reasonable time it works great. I've transplanted a few mallsai into hydroton and also coarse perlite, and also regular garden vegis.
I've had my hydroponic pre-bonsai's growing in the grow tent I built for over a year and a half.
p.s, you CAN grow a juniper inside (grow one, not just keep it struggling alive).
Your lights just need to bright enough and close enough without burning the foliage.
I've had my experiment documented at another bonsai forum; I just found this forum and thread a few days ago.
The pic I attached is the juniper in question, taken about 3 months ago. It's still growing fine, but slower since I changed lighting and moved it further away from the light's main focal area.