If Amir Johnson can look good on his role with the C's, I don't see any problem on putting Sabonis as a center.
The big difference is that Amir Johnson has a 7'1" wingspan, and even in his current state (with the foot problems, etc) he has a pretty good leaping ability.
His length combined with his vertical allows him to really bother shots in ways you wouldn't expect of a 6'9" guy. That wingspan allows him to get shots off against average NBA length quite well, and he only really struggles when he is up against guys with crazy length (e.g. the Aldridge's and Cousins' of the world).
My concern with Sabonis is that (like Olynyk) his wingspan is only 1" longer than Marcus Smart's, and only 2" longer then Terry Rozier's, and is actually a little shorter then Jae Crowder's.
If you look at Kelly Olynyk, he has the exact same wingspan as Sabonis and has similarly limited jumping ability - and you can see how much his post game faded when he moved from college to the NBA. At the college level Olynyk was an outstanding post player, because he was able to rely on his size to score over your average college bigs. Once he came to the NBA his length became a limitation, and his post came all but vanished. Luckily he has excellent ball handling skills and a very good outside jumper, and those skills have helped him get by despite the loss of his post advantage.
Sabonis also relies a lot on that "physical advantage" for his offence, and so I expect his posts game will also fade a lot in it's effectiveness at the NBA level. Unlike Olynyk though, Sabonis doesn't really have a lot of other offensive talents he can fall back on - he can't really depend on his handle or his jumper, as neither is anything special. That means if you take away Sabonis' inside game, you pretty much take him out of the game completely.
Maybe in time he could develop a nice jumper and that would help, but I still don't see him becoming much (if any) better then Kelly Olynyk, and you want more than that from a high lottery pick. From a late lottery pick, it's fine.