I understand your sentiment about bloating the bitcoin chain with non-financial data, but if the person creating the transaction was willing to pay for it (via tx fee) then why not?
Bitcoin is the first ever decentralized secure database that has potentially huge applications beyond just financial transaction (Decentralized ID being one of them).
If the core developers and community can expand the bitcoin technology to determine fair TX fee for non-standard transaction and size then it would benefit everyone.
If the proper fee can be managed in a decentralized way then we've really improved bitcoin; however, without this advancement essentially free non-standard transactions that are relatively big will not be favored at all. I have hopes that something will work out.
Remember: every additional use bitcoin has besides financials will ultimately add value to the entire system.
It's not a matter of "sentiment", but a matter of using the appropriate tool for the appropriate task. Also properly separating concepts makes understanding and evolving them easier.
There's absolutely no need to go through ugly hacks to insert this data inside the blockchain if you can create an alternative chain with merged mining. It would be worse for developers of your system, since they would have to find a way to fit their data into bitcoin instead of defining their own database as they please. It would be worse for miners that just want to mine one of the chains, since they would have to store both databases. Anyway, summarizing, these are different purpose databases, there's no need to fuse them. Just do it like namecoin people did it.
Plus I'm still not convinced you really need a blockchain....
The time stamp would be useful for an ID system as it could describe how someones ID evolved over time; however, the real appeal for using the blockchain is that it is a database that cannot be altered or controlled by anyone.
Why is it important to know which modification happened first, and why is it so important that you are able to know this without trusting anyone? As long as you can gather all data that there is about an ID, I suppose you're fine. Maybe I'm failing to see something, but I don't understand why a blockchain would be preferable over a distributed database which can't order things in time without trust.
Perhaps one of your motivations to use a blockchain is that the monetary incentives in mining helps guaranteeing that multiple copies of the database will exist. Plus it also adds an incentive against bloating it with unnecessary data, since it costs money to add data to the chain. I'm not sure how other distributed databases provide such incentives (anyone knows?). But if it's just for that, I guess you can come up with some sort of monetary incentive for those who "seed it", and some sort of monetary costs for those who add data to it, all that without using mining itself, which is very expensive. Blockchains come at a cost, and carry their own vulnerabilities.