I think that two things need to be addressed here; viruses, but also stealth.
Firstly viruses. I think that if you are able to get directly adjacent to an enemy, you should be able to virus them to your heart's content, boss or otherwise.. It should be a risk versus reward thing. If you take the risk of attempting to get that close and succeed, then your reward is being able to disable that/those bots. I DO think, however, that the virus is a little too strong right now given the wide variety of enemy bot healths and damages. Reprogramming the best bot on the field will easily win you the map as it stands now, especially given how little attention the enemy bots generally to pay to allied units, including turrets. To fix this, I think two things could be addressed. Firstly, make reprogrammed bots actually be shot at. This is an obvious one. Second, apply some kind of hard limit on the amount of mission a reprogrammed bot can be active, be it health depletion over time (-2% per turn for a 50 turn maximum?), ammo depletion over time (-1 shot per turn?), a straight turn limit before the bot shuts down, or maybe the reprogrammed bot can't move anymore. I'm not sure which of these, if any, would work.
Moving on to the second issue, stealth. Stealth is absurdly 'overpowered', though I loathe to use that word in the context of a singleplayer game. As it stands right now, it serves as a panic button (press button to not die!) as well as a number of free actions or turns where you are completely safe without fail from enemy bot attention. A large number of consecutive stealth actions / total stealth actions allows a player to clear an entire room with no threat, either by taking out the bosses using a couple shots then retreating and killing the rest as normal, by doing something stupid like filling the room with turrets / reprogrammed bots and then watching the havoc, or by using a long stealth-capable bot, moving into deadly melee range, and then switching to something else, like an epic siege or brawler. While I don't see a problem with those strategies in general, I think that stealth might be a little TOO safe right now. I mean, you literally can't die unless you kill yourself while stealthed, since all enemies basically shut down. Perhaps a small change to stealth mechanics is in order to bring the risk of using stealth (I'm moving really close to enemy bots) in line with the rewards (I kill everyone always forever). Something simple, like stealth instantly failing at melee range if you use a non-movement action perhaps?
This is a bit beyond the scope of this thread though, but I just think that virus wouldn't be so rampantly powerful if getting close to a powerful enemy bot was more of a challenge due to a stealth revamp.