Yes, me too. Scenario #1 is definitely most plausible. I've never opened a CGC slab before but I'd imagine it's not an easy thing to do and then re-seal to pass off as unopened.
But, Scenario #1 doesn't make sense with the book getting back out there again 2 years later. I'm with you in wondering why CGC just didn't take the book back instead of leaving it out there. Seems it would open CGC up to yet another buyer who'd need to be "compensated" for buying it. Unless, CGC did take it back but someone "inside" did some shady stuff.
This is why I take high-res scans of EVERYTHING I send to CGC (both front, back, inside). Whatever would help prove that what I sent in didn't actually come back. TMNT #1 is a highly sought-after book...and there are too many similar copies out there that can substitute for someone that isn't paying attention.
If what your fearing ever were proven to actually have happened it would end CGC. Something that has crossed my mind with other dealers but with CGC I think it's just paranoia.