Well, it has never been explicitly stated as such, but considering AS and CN are operated as separated networks, it didn't make sense for Samples to resign for an AS mistake, unless he figured it was better for him to fall than for AS (which has been a massive success,) to lose it's creator, mentor and head exec. His resignation stopped the controversy and kept Lazzo at AS. Considering Jim could have thrown Lazzo under the bus for it, and kept his job, there had to be a degree of taking one for the team.
Of course, that debacle means that Lazzo will never get to run the whole network (as internally I'd have to guess they recognize it really was Lazzo's responsibility,) and the fact is, he's one of the only guys' left who might be able to make the whole thing come together again. Though, I hear Betty Cohen isn't at Lifetime anymore, and if they can get Fred Seibert back doing work for CN, I wouldn't rule Cohen out.
Probably won't happen though.
Besides, even with Samples, Toonami might still have ended up in the can, and we definitely would still be looking at a live action line-up. He was ultimately a good person, but he still isn't what the whole network neeRAB. The network neeRAB someone with Jerry Beck's love of all animation and Herb Scannell's business saavy in regarRAB to cable TV. CN had those people pre-Time Warner merger. Probably never again.