You will create the exact same problem you want to fix: we can guess
some softwares are built on linux/m68k with 2byte alignment in mind. So
once the ABI is changed, you'll have to track them to fix them.
Could you point me to these packages which assume 2 bytes alignment? I'm genuinely
interested as I would like to put these up on the wiki. So far I haven't found any.
I have used Debian's rebootstrap to create an initial set of m68k packages with
4 bytes alignment and didn't run into any problems yet.
The Gentoo developers have also successfully created a chroot with 4 bytes alignment:
https://dev.gentoo.org/~dilfridge/m68k/
I have tried it and it worked fine for me with qemu-user.
So, if there is any software that is incompatible with 4 bytes alignment on m68k, I
would like to hear about it.