I wouldn't mind them starting from the first episode, but the problem is Toonami's current format of airing 1 episode per week would work against the series since stuff doesn't really pick up until around episode 30-ish or so.
The whole 1 episode a week thing is working for the rest of the Toonami shows. "Bleach", "Naruto", and "Soul Eater" are all doing very well. As far as having to wait 30 episodes for the series to pick up, is it really that big of a deal? That's how a good story works, you build it up and build it up. Even "Naruto", as much as people say it hooks you quicker than "One Piece", took a while to build up.
The only reason Naruto's is starting from the beginning is because these episodes are being re-aired "uncut" for the first time and Disney still holds the rights to Shippuden. They didn't reset Bleach despite the long hiatuses so it makes sense if they want to avoid resetting One Piece.
I will say that if the rights were available, I'd say Toonami probably would've picked up "Shippuden" sooner than the original "Naruto". But by the logic you're using with "Naruto", to appeal to viewers by re-airing uncut for the first time, "One Piece" airing from the beginning would have more of an advantage than "Naruto". "Naruto" aired almost all its episodes on Cartoon Network with very minimal edits compared to a lot of the other anime that aired on Toonami, plus a fairly accurate script. On the other hand, most of what we got with "One Piece" on T.V. was the 4Kids dub. So in that regard, isn't it blatantly obvious that "One Piece" uncut on T.V. has more to gain than "Naruto" uncut on T.V.?
Also what argument are you trying to make with "Bleach"? It's just a long-running show that's continued to run new episodes since it started airing on adult swim, and then it takes breaks. Seems irrelevant to me.
But the basic problem is…
The current Toonami is not exactly the most appropriate format to run long running Shonen shows. It works for shorter series, but they really need a Mon-Fri thing going for anything over 52 episodes. Bleach gets a pass because it's been running continuously, but Naruto is kind of "just there" because Shippuden couldn't be acquired.
It's not ideal to air a long-running series once a week, yes, but it's been working with "Bleach" and "Naruto", very well. But these reasons for why they're "exceptions" doesn't make sense to me.