I wrote an add-on to re-stack split stacks in the guild bank. It's not polished at all and has a minor timing issue that results in some items not being re-stacked properly, which I will address in the near future along with adding some sort of UI. At the moment it is just a slash command.
https://github.com/snarez/FatStacks
http://esoui.com/downloads/info335-FatStacks.html
Not sure when I'll get back to working on it, so I figured I'd drop it here in case anyone else finds the guild bank stacking as annoying as I do.
Note: I'm about to change my github username so I'll update the link when I do
Edit: Added link to esoui page