Disk repair failed after using OS X with hibernated Windows/Boot Camp with MacDrive

I forgot I just closed the lid of my MBP the last time I used Windows/Bootcamp (instead of shutting it down) and that triggered hibernation.
The next time I powered my MBP on, OS X started automatically and I opened some of the same files that "were already open" in the hibernated windows (on OS X main/boot partition, using MacDrive in windows).

That (or resuming the hibernated windows later) probably led to some data corruption that prevents the OS X volume from booting and neither the automatic repairing during booting nor disk utility (external hard disk drive or recovery partition) is able to repair it. I am not sure if there is any difference.
Booting in verbose mode shows the file names that were double-opened during repair attempts.

After booting OS X from an external hard disk drive, Disk Utility fails mounting the main OS X volume straight away. But succeeds with mounting it after a failed repair attempt. I only have read access then, though.

Bootcamp partition is still working fine.

1. I wonder if it is possible to gain write access somehow and if deleting just those "double-opened" files/the containing folder (which is saved on Dropbox, so I really wouldn't mind deleting them/it) would solve the whole problem or if i really have to reformat everything and spend 10+ hours to revert everything to the state before the data corruption.

2. If I have to reformat + reinstall, using migration assistant and the corrupted volume as source isn't a great idea, I guess? Are there any options to exclude some specific folders of the user folders?

3. Will the Bootcamp partition work after reinstalling OS X or do I have to winclone-it somewhere? Checkdisk says the volume is OK.