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Yes, MCServer doesn't care about existing blocks too much. It doesn't crash on unknown blocks, but it doesn't know how they interact, either, so for all its purposes such blocks behave just like stone.
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Should MCServer really allow unknown blocks? What about the other clients that don't have the mod installed? I think that will make them crash.
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I believe that's the same with the vanilla server - if you give it a world with unknown blocks, I'd expect it either to crash itself (if it doesn't have the mod installed), or the client crashes when it receives the world (and it doesn't have the mod installed).
I don't think MCServer by itself should do any kind of data sanitizing, because, after all, you can write plugins that can provide the mod functionality, so it can work with the modded clients. Of course there's still the issue of non-modded clients crashing, but hey, there's no solutino to that.