Yes, sorry to say, but Marth will probably be your best choice against MK. Snake can fight MK without being "pwned." Really depends on who you ask, but even if people say Snake is better against MK than Marth is against MK, Marth would still be a better choice simply because you don't have to learn a completely different character.
DDD, Falco, and Snake are some of the better secondaries. I recommend DDD though, as he deals with Snake well, which is, although may be even, a tricky matchup for Marth.
There's also a thread around here in the Marth Boards that explains thoroughly how to counter MK in many different situations.