It's probably possible to make a script which replaces the contents of your reaper-kb.ini file, which contains your key mappings. But that is a pretty crude workaround and unnecessary for what you want.
Instead, what you should have in my opinion is a script which either triggers Play/Pause or Play/Stop depending on an ExtState, which is a kind of variable that you can store with ReaScript to set persistent states. You could set such an ExtState with a toolbar button, just like in Pro Tools.
It's a pretty simple script, if you ask in the scripting subforum I'm sure someone would be able to help you out.
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