I can see why people don't use bcrypt/PBKDF2: they don't know or it's not a priority. Your reason, however, doesn't strike me as a particularly good one: you could just write a quick password reset tool in PHP or even better write a quick shell script that splits out the password reset query.
I'm I guess a little hesitant to follow up on these because the original post is getting strongly downvoted, but I tend to agree somewhat. This is the same as I was telling people at the company -- "just use the PHP API we've developed!"
It turns out that this is a bit complicated, as my colleagues readily pointed out to me. So for example you are basically saying "write a .PHP file and execute it locally," which is perfectly fine, as long as the problem comes from your boss or one of your testers -- it is risky when it occurs on a production server (because the script you're generating is insecure). On your production server you really do want to execute the action from within a MySQL prompt if it's possible, and so it's a sort of two-sided game of "I'm going to reset my password over here and then update their (salt, password) with the result of my local PHP queries," and that's a bit weird as a process.
The other tender point is that once you've made a choice, it's very hard to change it. So, "all of our existing passwords use the old system, we're not changing!" was a very strong argument and I did have to spend a bunch of time creating a fall-back for legacy passwords.
I would agree, however with this: in general there is a reasonable expectation of, "if we're doing this so much that it bogs us down, then the app is mature enough for a proper email-sending password-reset tool; and as long as it doesn't bog us down we'll do it the hard way." But convincing people to make the hard way even harder is a tricky proposal even on a good day. It's like telling people, "no, leave that code, I know it does 2^n operations but n is always small and it's not actually the part that slows down our system and it's more readable this way." The intangible -- security/readability -- is being negotiated for the tangible -- dev-ease/speed. I had trouble selling it to the other devs.
And I think LinkedIn really has no excuse.