Yeah, I guess it depends what you mean by invasive changes to BitCoin. It does mean changes to the software, but only a couple of new RPCs really and a few tweaks to the getwork protocol. The changes sipa is making to handle wallet sharing, per-txout spent tracking etc are far trickier and more invasive IMHO. Which changes were you thinking of?
At some point somebody will add the necessary RPCs and put together a little framework for the alt-chain side, then I think a lot of these sorts of discussions will peter out because it'll be so easy to do things the right way. Heck, maybe I'll do it, if I get some time this summer and Vince doesn't beat me to it.
With respect to ECCs and such, I think it's worth taking a step back here. To fend off abuse you don't have to make it impossible. That's hard because there's always another move that can be made. To win all you have to do is make abusing your systems less appealing than using the alternatives (eg, freenet).
For storing files in BitCoin specifically, it's already pretty unattractive and that's with nothing more than the IsStandard checks. Making it harder is easy - we already established that you'd have to encrypt your data, which means there needs to be a side channel telling the recipients which transactions to read and what the keys are. If you have such a side channel, you probably don't need the block chain at all.
What's more to receive the file, now everyone who wants it has to download and process the entire block chain, a process that already takes forever just for financial data.
So it's expensive, slow, complicated .... I can't forsee a time when BitCoin makes more sense than Freenet or BitTorrent, etc.
One obvious thing for people to store in the block chain is their encrypted private keys. That's only a few thousand bytes, and after doing that, they can burn their PC and their wallet, and get everything back on a completely fresh machine, and never have to worry about losing their coins.
There might well be schemes where this sort of thing makes sense, yes. To be clear, I don't object to storing things that are essentially financial in nature in the block chain - that's what it was designed for and it's good at it. In future we'll see transactions that represent multi-party contracts and such.
This specific idea doesn't make sense because if you encrypt one set of private keys, you end up with just a different set that also have to be stored. If you then burn your computer you'd lose the second set so you're no better off than you were before.
I think what you want to achieve can be done with password protected transactions. It'd need to be carefully designed to make brute forcing very slow, but if you did the work to support such transactions, it'd certainly be interesting and worth considering for inclusion.