Just to be sure I understand you properly: this is about the right to erasure (a contact ask your organisation to remove any data about them), right?
It's my understanding that indeed you should remove the data both from the live and the log table (as the later isn't a temporary backup but long term archive).
I recall a discussion about changing the format of the archive tables (so the engine isn't ARCHIVE anymore). The impact on the size wasn't that bad for what I remember, so it might be an option.
ALTER TABLE my_table ENGINE = InnoDB
And the only one I can think of to be able to be compliant.
I'd suggest you to check on a backup first, there is a ROW_FORMAT=COMPRESSED
option, but it seems you need to tune your install a bit to benefit from it on a per table basis... and it might not be needed, based on the size of your installation.