Tampering with someone memory without their consent is a violence pure and simple, and it doesn't matter the reasoning behind (and even if the case was for her own protection the point is logically invalid in all the different interpretation). It's even more serious then phisical violence imho, as memories are what the mainly define us.
First of all concentrate on the reasoning: it was made to protect her. This is an illogical point for different reasons. If we assume that the point was becouse she may be targetted for the engagment or the position of prince's wife then just breaking the engagment would have sufficed. Wiping her memory does NOT offer her more protection. If instead we think that she may be targetted for her significance to Will, as a way to control him, than wiping her memory doesn't actually protect her becouse it's not HER the target but HIM by proxy.
It's also clear that the altering left her with a dissociate state between reality and her own memory. This is not good for someone mental health, expecially during the maturing phase. So he actually hurt her instead of protecting her. (It also cuase her to phisically suffer, as shown when she caught a glimpse of the erased/suppressed memory)
There is also another point that is often overlooked in memory altering scenarios:
How do the altering works? It just suppressing/erasing a certain amount of time (assuming memories are stored sequencially and "timestamped")? This is certainly bad and if done for a high period of time highly disruptive. But altering specific memories (as removing the memories involving Will, or altering the ones were Will was present with other peoples erasing Will presence ) how do work? Doesn't it require to "access" (and thus see) these memories (and also unrelated ones)?