There is no problem getting a restricted medical with a colour vision deficiency. The restriction added to a class 2 (or even class 1, see my earlier post) is not "day VFR only" as some previous posters have suggested, rather it is "flights by day only". It is perfectly possible to fly IFR with a CVD restriction and I often do, using my IMC rating.
There are some other restrictions as well - you must have a radio for flights from and to airfields that have ATC and for a class 1 certificate, no commercial air transport is allowed.
The sad thing is that if the IMC rating is killed off for new pilots then the potential safety benefit of instrument flight will be denied to anyone with CVD because they cannot currently get a full IR. This is clearly very discriminatory, which is why the night qualification is not a pre-requisite for the proposed modular and en-route IRs. I would not hold my breath for these last two to be introduced though, as I understand some airlines are against them.