I suppose whatever you want to run is up to you.
Personally, I think Gamma World works best as a D20 system. I remember the original Gamma World rules, and they were always a bit tongue in cheek. I think Gamma World is best run as a kind of spoof (even if it was originally not intended to be).
And the thought of a Mark V blaster hit to the right arm is not something I'd look forward to as a PC.
Still, if you want to run Gamma World as a Runequest game, anything is possible. I can't think of any specific recommendations offhand. Perhaps rules for radiation resistance can be based on rolling Con or less on D20, with modifiers to express how severe the radiation is, since resisting radiation is not really a skill that you can learn.
I suppose another argument for D20 Gamma World is that the way D20 handles templates makes it easy to figure out stats for mutated animals and characters. For Runequest, you'll have to develope something like a template concept, although that shouldn't be too difficult.
In another thread I started a discussion of defining advantages and disadvantages for Runequest -- these would work well for mutations. In my Runequest Modern campaign I plan to have the PCs roll 4d6 drop the lowest for Advantages, to determine the number of points they can spend on advantages. You could do a similar thing with mutations, or allow mutations to be bought as advantages and disadvantages.