What tools/software do I need?
010 Editor. 010 Editor M2 template. MPQeditor.
Can this get me in trouble or compromise my account at Battle.net?
Technically, yes. You're altering the game files. Probability of being caught? Basically nill.
If so, how do I circumvent that and still do it? Possible?
Such a low chance that I wouldn't even worry about it.
As for the how-to, it's been a while since I played with animations. I think this is probably too advanced for you without background M2 modding experience. If I were doing it, then I'd to copy the swimming animation sequence twice, point them towards the correction animation IDs for walking and running, remove the default walking and running animation ID pointers, and probably have to mess around with some other values in the M2 to make it work correctly.
It's definitely doable though.
[Edit] After taking a quick peek at it, it may be easier than I thought. Editing some pointers may be enough.
[Edit2] Looks like more than just pointers hah.
[Edit3] PhillipTNG's post from this thread:
viewtopic.php?f=7&t=7798&hilit=animation+swap&start=15 indicates it's more complex, which matches what my testing from this morning tells me too. It doesn't appear to be just swapping stuff around like Alastor's post in that thread suggests.