Late entry for rebuys is a no brainer. That will work. For what that's worth.
Without blocking IPs and disallowing tor (not even possible?) I don't see a solution for regular tourneys. In that case if you want late entry you just have to deal with the reality it's a rebuy for shadow accounts.
1) bust-out IP block is a easy way to cut down. Many players use VPN though.
2) I would imagine a savvy degenerate (that busts in the first 1 or 2 levels) may find their way back in. This may be something we must accept (from a player perspective I think its a great thing if a guy that just fired off the stack in level 1 re-enters) if we want to provide the utility to players that just missed the starting time and want action. I think that utility far outweighs the unfairness of someone possibly re-entering.