I don't have MNK above 50 so I haven't used Second Wind since then; however if it has not scaled to take into account our more then doubled HP totals, then it should also be boosted to reflect that. A 50 MNK with 6k HP healing themselves for 1.2k wasn't game breaking. Making it so the 10k HP MNK(or cross classed jobs) heal for the same percentage now that we have so much more HP would also be acceptable.
If SE had bothered scale various thing with the expansion, this wouldn't be an issue. Sadly, they didn't look at a lot of them, at all.