- Excessive clones drain the server's resources and bandwidth.
- Trolls often register multiple accounts to carry out their activities (to carry out a one-sided discussion, boost support for themselves, etc)
- In Marketplace, clone accounts are used to artificially boost prices and a seller's standing (it has happened numerous times before we clamped down on clone accounts)
There are more reasons but off-hand these are the main ones I can think of. So yes, giving benefit of doubt is nice, but the problem is that people will (and has time and again in the past) taken advantage of CS's leniency to push the limits. Now, when we have reasonable... erm, reasons to suspect clone accounts, we close them after some investigation.
If anyone has any questions or you have or know people who were mistakenly deregistered, I encourage you to drop a email to firstname.lastname@example.org.