Small Joint Training
The doctor is right in practicality, if not in technicality. If you have a weight bearing bone, it can be thickened, if you have muscle that you have conscious control over, you can exercise and strengthen it.
However, the amount of work and time to improve it will be vast and then it still won't mean much in the face of full body weight throws, etc. Making a pencil twice as strong doesn't matter if it gets run over by a truck all the same.
You can try to do things to protect your toe from re-injury, which may include taping, braces, limiting the type of training, but that's about it. It's a small joint, and a key part of many grappling arts is using full strength/leverage against small joints just because there's practical limits to what you can do to protect them.
Training to Avoiding Injury
Whole body strength training is great. Swimming is a good option. Give your body time to recover and build muscle. Yoga can be a great option as well, if you focus on stabilizers and making sure you have strength along your whole range of motion. If you get flexibility but have no strength at your need end-range of motion, you simply open your joint up to instability and risk.
Particular for grappling arts is to be mindful in training - tap out early if you can't get a way out, make sure your training partners are operating with an appropriate amount of speed to their skill level - getting cranked too hard is a great way to get permanent joint damage for no real learning value at all.