When you say "Maybe the current anti siphon is bad?" are you referring to the anti-siphon component of the toilet valve, or the component of the brass valve back on the pad? Either way, that wouldn't contribute to algae in the pool. I'm not sure how any leak would. A leak implies water leaving the pool, not ground water coming in. I suppose water could get in from outside the pool, but I don't think that's likely. The pressure of the water in the pool, above the leak's elevation, would force water out. Let me know if I'm incorrectly interpreting what you're describing. Beside, if your auto-fill has been running, that confirms water is
leaving the pool. The water the auto-fill was adding would have been city water, free of algae, unaffected by the presence of any anti-siphon component, even one that is defective. So that is not the source of your algae issue. Not sure what your pool guy was getting at. If he is anything like my now-fired pool guy, they just make stuff up to explain things they know nothing about. (Like me!!)
There are plenty of reasons algae can be a chronic problem, and we can discuss that when you're ready to tackle it.
I'm not sure what the best epoxy is for this. Not even 100% sure it would be an epoxy. I just know PVC glue is not the right stuff, so don't use that. Do you have a local West Marine store? You'd want something marine, something a boater would use below the water line, in salt water. A glue that will stick to PVC and whatever the toilet valve is made from. The marine industry will have the right stuff for that. You could even test that. Assuming the well is PVC (do you know?), you can test your glue with the old toilet valve part and a PVC fitting. Don't try to match the threads, you won't be able to. Just see if the glue you want to try will glue a chunk of PVC to the toilet valve bottom. You'll be able to tell if it makes a strong connection or not. Then you'll have the confidence to use it on the well.
Depending on what the return is, it may unscrew out of a socket. Those are typically 1.5" PVC threads and you can use a PVC or ABS plug in the socket with some teflon tape. Like this:
If you can't make that work, or don't want to mess with trying to unscrew the return fitting, you can cork it up with one of these:
You have to get the right size, or buy a few, or an assortment, and use the one that fits best. One of those two solutions will plug up the return. Need I caution you not to over tighten? (Sorry, couldn't resist!

) Then you can wet-vac or sponge out the well until it's dry. You'll be able to make good use of that extra mystery valve back at the pad: shut off both valves to the auto-fill supply pipe and hopefully one or both will shut that pipe down completely.
Again, if this was my pool, I'd toss the old toilet valve, and buy a new one, or rather three or four new ones, so that you have a fresh start and all the backups you'll ever need. By the way, they're not actually toilet valves, as a toilet valve won't work for this application, so don't just grab one of those off the shelf at Lowes. They make a special type for pool auto-fillers. I cannot now recall what the difference is, I just know they're not the same thing you put in a toilet. I shouldn't have been calling it that, but it made for an easy reference. So step one is to see if the existing one has a part number, then track down its replacement. Be sure what you buy is meant for a pool auto-filler, and that you're not inadvertently replacing an actual toilet valve that the previous owner mistakenly used.
I can't think of a reason all of this won't work, but I was already wrong before, so we're hoping others will review this crazy idea to see if they can site a flaw.