I think this isn't a situation where you should have to choose between those two outcomes (buying skills shouldn't have weird indirect nerf outcomes)! I'm not sure what the best solution is. I have a couple of options:
Option 1:
The melee damage prayer results only apply if you've got a physical or innate melee/h2h weapon that isn't disabled in the weapons tab AND the existing skill check. Characters who want to use touch spells can make it happen, characters that dont mind can keep a weapon and just go with the flow.
Option 2:
The melee damage prayer affects touch spells Probably OP? Not substantially more OP than the other results I guess
I'd suggest just going with option 1
