The spell itself is powered by another witch, not the one being reincarnated. (After all, the one to be reincarnated is trapped in the crystal.) This makes the reincarnation candidate vulnerable.
1. If I'm the #2 witch after the now-deceased #1, there are a couple of factors that would influence me. First, a powerful soul trapped in a crystal might be useful for creating powerful magical items. (For me, of course.) Second, if I'm #2 but I can become #1 by an unfortunate and unforseen accident happening during the reincarnation, where exactly is my motivation to succeed? I would of course selflessly take up the burden of continuing the master's studies...
2. The one performing the ceremony might honestly fail. They are the apprentice (or competitor), after all.
A second line of options would revolve around the actual takeover of the host.
1. The host's soul may in fact overpower the reincarnated one -- it is their body after all and you can have a strong inner will without being magically powerful. So the reincarnation candidate has to deal with the distinct possibility that they will will be the victim rather than the victor. 227
A lifetime of magical training, handed over to some peasant who happened to be strong on the inside. (This raises the additional plot point that it may not be easy to tell if the ceremony worked one way or the other. The victorious host would have access to the witch's memories, remember.)
2. The witch doesn't subdue the host once for all time. Rather, they must dominate and work through the host. If the struggle is too severe, the host could be mentally damaged so badly that the witch is trapped within a barely-functional host. Sort of like a sharp mind trapped in a disease-ravaged body. Not to mention that the constant fighting and need to domineer makes the reincarnation less desirable than it might otherwise be. Only the supremely (over) confident would attempt it.
(And this is a key point: if you do the ceremony, it works, you take over the body with no risk or pain and the previous owner is at your beck and call, it's hard to see how it wouldn't be enormously popular. There has to be a downside for the witch and I like the idea that they continue to exist and gain power, but it's not a pleasant existence.) 227