I completely agree with the fact that Assassins can be very helpful to their team, but what I'm arguing is that the game doesn't discourage any kind of meaningless solo play even though it should.
You could chalk it up to player fault, but I don't think that works in every case. Couldn't any imbalance in any competitive game be chalked up to the player not using something properly or other players not being able to cope with it? No, I think there's a point where it's actually the developer's fault for not curbing poor player behavior. After all, that's really the point in balance, and influencing player behavior is exactly what happens when developers talk about "discouraging such and such" or "encouraging team play" or what have you. It's tweaks in the balance that nudge the players into playing a specific way.
I'm not seeing any of that with the Assassin. The reason why so many Sins are terrible as you say is because they think, to quote Yahtzee () "You CAN but why would you want to?" Sins CAN push lanes very effectively. They CAN smokebomb turrets, and they CAN distract other pros. But why would they want to? They have no incentive to actually push the team beacuse they get just as much satisfaction running around and just killing everything in sight.
Class-based team games operate on the Strengths vs. Weakness design for that very reason. They make class X good and this thing but not that thing, and class Y is good at that thing but not this. That's why acting as a team comes a lot more naturally to the other classes in MNC, because they have weaknesses and strengths and rely on the other classes to do what they can do. But then look at the Assassin, who doesn't need absolutely anything to have a satisfactory experience in the game. It's the solo character that doesn't NEED to play by the match's rules to kill bots and pros and move all over the map and destroy turrets and everything else. That's the problem with the Assassin, and why Uber needs to think along the lines of making tweaks to the gameplay to get people to actually play as a team with that class. It's not that she CAN'T help the team, it's that she doesn't need to, and because she doesn't need the team's help either.
None of the classes need teamwork to be successful. Each are strong on their own. Snipers can camp, Tanks can single handedly lane push. Supports can lock down areas and camp there, Assaults can be anywhere at any time, and gunners are killing machines. A team using teamwork though is more powerful than these pros working alone, and the Assassin is no exception. They need their team much more than you think. While they're clearing lanes you might as well attach a massive "shoot me plz" sign on their back and have them wear a chicken suit because the assassin is wide open for anything to come their way. They either have to escape or die being as fragile as they are. Even clearing lanes will suck the health out of you and it's very possible to be bent over by the very bots you were clearing out without the Gold armor endorsement. While they go after turrets it's the same deal, only they'll need additional backup for more powerful turrets and defending pros. What they need is for their teammates to make openings while they make the starting/finishing blow.
Why they would do such a thing is a part of being a good player. The incentive is to help the team. It's the same with the support with his heal/hurt gun who only benefits from a little bit of juice building when he overheals folks around him. Bad players being bad is just down to that, bad players. Look at the TF2 Pyro. W + M1 is not proper ambushing and flanking, though the class suffers in that department anyway. Besides, your logic can applied to me just playing any class how I want. I can be a deploying tank camping our upper base on a window and railgun everyone if I felt like it. I could be a camping sniper racking up the kills sitting in my own base and only laying traps around me rather than booby trap where my support has set his sentry and snipe on the move. While Assassin players could use a bit more direction, I don't think its a major issue outside the name which implies pro killing. It's like the scout from TF2, who aptly fits the assassin moniker being the best combat class in TF2, rather than the fast/light hitter like his current name suggests.
Sure, you can ninja your way behind a base like in Spunky Cola to destroy bots at the source and get rid of longshot turrets all by yourself. You're still helping the team by doing that, and it's akin to the Spy taking out unguarded sentries.