Essentially, Orange and O2 are convinced that offering a Skype client on a phone leaves an avenue for customers to pay less to their cell providers, which they see as hitting their bottom line. As a result, it seems they are threatening to refuse to carry the N97 on their networks unless Nokia agrees to pull the application. A bit late, you'd think, given the current state of the market. If they do get their way, however, it'll really only be the user who is hurt – with a phone artificially deprived of functionality due to a carrier's whims.
Internet connectivity will only increase, and VoiP technologies will be more heavily adopted as a result. Though it's rare now, we may eventually see a large market of cell phones used for VoiP exclusively, cutting out a cell provider altogether. Orange and O2 are definitely working backwards here, and it would be better for them to try and adapt, perhaps even offering VoiP services themselves rather than trying to impose their will on manufacturers and consumers.