I see no reason to think that the actual election in November won't also be rigged to the maximum extent possible for Clinton.
And, again, in the general, I've seen no evidence that the Clinton camp is vastly less moral than the GOP/Trump camp- why attribute all potential rigging to Clinton when the GOP has just as much reason to pull the same tricks?
I just don't see how, if widespread primary rigging is effective and not all that difficult (since the DNC, who really aren't all THAT clever, supposedly "rigged" it without much in the way of repercussions) Trump could end up the GOP nominee against the wishes of the GOP elite.
It's quite easy to explain Clinton's win without any shady "rigging." It's quite difficult to manufacture 3 million net votes- that's either a lot of ballot-box stuffing or a huge voter disenfranchisement campaign and there's no evidence of either. The simplest explanation is that the Dem constituency consists of people who want her.