The tape over buttons is a good idea..
Also, I have seen older models that have rotary, analog timers, like the old minute minder type of kitchen timers that you twist the dial, and it mechanically dings after the spring mechanism winds down. You may also be able to find that type of control on a very bottom of the line, dorm room type model at Walmart of Kmart.
I believe those timers go higher that 45 seconds or a minute, but it seems to me that it being a mechanical twisting dial would make it infinately easier for an older person to understand it, and to operate it properly, and not set it to keep on running. You could put a piece of bright tape and teach her to not twist it past that spot. Or you could even devise a mechanical stop so you could only twist it past a certain point.. maybe even mold a crude stop out of epoxy putty, stick it to the faceplate next to the twist dial, but have it stick over the dial so it prevents the dial from twisting past that point.. I am describing it inelloquently, but a typical reader of this group could jimmy up some sort of stop without too many problems.
I would guess she makes it go to long because she may only know how to get it on, but may not fully understand how the set the timer to have it turn off automatically. Which I fully understand, those buttons can be confusing for me, and I am a mensa member* in the prime of my cognitive life.
*author may be exagerating the facts, or just making stuff up.
Another suggestion, if it is truly just for her tea, what about picking up an electric kettle, it looks like a typical tea kettle, but has a base that you plug into the wall, It heats up quickly, then you pour out the boilding water. The advantage is those have auto shutoffs if they boil dry, so even if she left it on, it would pose no danger. then she wouldn't be using the m-wave, and have a safe alternative.