I would not worry about the alignment issues at all. The problem is that
one of your disks is having bad sectors which still need to be
reallocated. That means you may already have data loss. Chances are that
the number of bad sectors is going to increase over time which is going
to lead to more data loss.
My personal advice would be to replace the failing disk with a new one
and restore from a known-good backup. If you lack money, you can try to
find a used disk, but I would only pay for something which I have
checked with smartcl beforehand. If you lack a backup, you can only hope
that you have lost nothing of value and get a new disk as fast as
possible.
Personally, I don't think it is wise to throw away any HDD as soon
as it gets a few pending bad blocks for whatever reason.