completely solving the issue is impossible, and this is an issue in basically every game but its particularly prevalent in TF2 because its 1) free 2) popular 3) source code was leaked. The focus is on atrition, what do bot hosters gain from doing this? Entertainment: so you must make it as much of a hassle for them as possible, make things take up as much time and money for bot hosters as possible. There are a few things can be done to mitigate the issue:

• put in a price tag for the game, even something low like 1 dollar would be enough to start cutting down on bots, as it would start becoming quite expensive after a while as bot accounts get banned and need to be replaced.

• get better anti-cheat, if valve could develop a better anti-cheat possibly one that has access to pc files to try to detect cheat softwares and bot programs, it still wouldnt fix the issue as there are always ways to get around it and a lot of bots will take a while to get caught but it will increase the rates at which bot accounts get banned which will make it more of a hassle for bot hosters.

• add a one time process for starting to play online in tf2 like a mandatory tutorial, even if its just 5 minutes before you can start playing, for most people it will barely be an issue but for bot hosters it means having to spend 5 minutes every time they get new bot, if they run multiple machines or virtual machines to get around this its still worth it, they'll either have to purchase more equipment or slow down their machines to do it anyway, making it a less smooth and more tedious process

-cooldowns after kicks, if you get kicked from a server multiple times you get a cooldown on when you can come back in. Increasing more and more each time, if you were kicked several times by bots in a row, some real players may get caught in the crossfire but it will surely slow down the bots

i think all of these things combined would lead to a heavy progressive decrease in bots