I have to port source code from to an ARM platform that runs Linux. Unfortunately I have run into unaligned memory access problems. The source uses pointer casts and access
Wow, that's an unholy mess. Fiddling with the compiler isn't going to get you anywhere. The code is illegal on ALL architectures, but just happens to work on some (e.g x86). I would fix the code itself.
Sadly there's no pretty way to do that. However, you might get a long way with a long list of search-and-replaces, then manually fix up the rest. I'd start by removing the declarations of those data types, so if you compile any code you missed, it'll error. Then, search-and-replace snippets such as "*(IEC_DWORD OS_SPTR *)pSP =" with "set_dword(pSP, ". Make an inline function "set_dword" to do the right thing. Carry on for as many easily replaced snippets as you can imagine. There will still be a large amount to fix up by hand.
The only other way I can think of doing this would be a compiler plugin, as you suggest, and make every pointer in the entire compilation unit have alignment 1. The compiler will then byte load/store everything. It'll probably end up doing that for more than just the code you intended. This probably isn't as easy to achieve as it sounds.