We haven't seen the full extent of Ceph technology (in Crysis: Legion the Ceph in New York were described as gardeners rather than soldiers), so at this point it's hard to say. Judging by what we have seen, though, the Covenant would squash the Ceph easily. Covenant soldiers often perform EVA operations and they have dealt with infectious spores in the past (i.e. the Flood), so biological warfare that's non-contagious would quickly become useless against the Covenant, once they realize what's going on. The Covenant have highly damaging plasma-based weaponry and various others as well, while the Ceph are limited to ice-based weapons (which are no better than bullets against energy shields). Ceph heavy weapons don't fire rapidly, while the Covenant have heavy weapons that can fire as many as 5 shots per clip. Add all this to the fact that the Covenant can destroy the surface of any planet via orbital bombardment (aka glassing), and you have charred squid remains.