I'm hoping that, secretly, Rebellion are already talking to comixology and they're building a 2000AD specific reader that includes subscriptions -but I'm a dreamer...)
If not, they're bat-shit crazy. Seriously. Comixology is the only place to be on iOS, and even DC has finally figured this out. With the way Comixology works, 2000 AD would be part of the same thing that pretty much every other major and indie worth its salt is involved with *and* there's potential for an alternate own-branded app (like the DC and Marvel ones), trades alongside single issues, digital-only specials, and so on.
By contrast, Rebellion currently has Clickwheel, which isn't optimised for iPad and was last updated... on October 9, 2008. Great.
(Also, joining Comixology needn't remove Clickwheel anyway, in the same way that 2000 AD being sold in WHSmith doesn't stop subs going through FPI or sales happening through other retailers.)