The problem with things like irccloud from a network operator perspective isn't that it's difficult to distinguish between users. It's that these systems often subvert protections the network has deemed necessary.
Imagine example.net runs an open proxy scanner on anyone that connects. They find this reduces abuse considerably. If (e.g. irccloud) either 1) doesn't pass the originating user's ip 2) isn't trusted to pass the originating user's ip or 3) doesn't run a similar open proxy scanner, then example.net's open proxy scanner solves nothing.
1) isn't always technically trivial. 2) isn't for us to decide and 3) is probably never going to happen as the network will likely always be ahead.
If you do manage to solve 1&2 between a mitm & a network then awesome. The problem is that this requires buy in from both sides. Just because irccloud.com support it doesn't mean it will automatically work on any irc network you try and connect to.