Yes, clone is removing all active spells from caster now.
Almost all, actually.

Some strength booster is still in effect, divine strength from Paladin, I guess. It was removed from active spell list, but stats were still in effect.

Also, long term - extradimesional manipulation - is not interrupted when clone casted. But you couldn't see $lt in promot anymore (you still see each tick though). And you are allowed to train skills like you do nothing at the moment.

Oh well, on other side it gives some advantage to be SM, making them a bit closer to power of other semi guilds :).