First, if your PU called obstruction on a runner, please send him back to umpiring school.
Now, assuming he meant INTERFERENCE, you have 2 outs, out at 2nd, out at HOME, R2 back to second, BR to first.
Now, your other question is, SHOULD this be interference. This is a judgement call, and definitely HTBT. But I would point out that this is YOUR call, not his. I would also point out to you that the runner cannot stand up into a throw. The runner has no rights at all except the right to not dematerialize. This SOUNDS like interference to me, but again, it's HTBT, and it's your call.
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