Wouldn't there be some way to discourage miners from solving a block with malleated (or should I say mallified :-) ) transactions?
Some forms of transaction mutation, like the ECSDA sign-inversion mutation, can't be distinguished from the original even if you have both of them side-by-side.
There are other forms of mutation involving alterations to the script. There have been proposals to prohibit obviously-mutated scripts (like scripts with a bunch of no-ops stuck on the end), but going beyond the obviously-mutated scripts risks accidentally banning useful scripts or future uses of the script system not currently foreseen.
A middle ground is to come up with rules for preferred transactions (ECDSA sig has the preferred sign, DER encoding, only very basic scripts) and hold any non-preferred transactions until the next block to see if a preferred spend of the same outputs shows up. But you can't force miners to do this and it's slightly contrary to their interests since they'd have to forego the transaction fee. Cooking up new rules also isn't the sort of thing you want to do in a crisis like the current situation.
I was under the impression that the Sign conversion / Modulo change of the signature was immediately obvious, because the default client would only choose positive R and S and there is only one other solution in the available length.
Maybe the majority of miners could cooperate to block the spending of matured coins from a coinbase of a block that contains more then the usual share of malleated transactions by not accepting it in a block for mining. Then the original miners would have to spend a double effort to spend their coin.