I don't know. I don't think he deserved to die, at least not without a fair fight. If it is possible to qualify evil by quantifying evil acts (like killing, for instance), then I have to say that Lindsey would have been one of the least evil people standing in that alley. Lindsey was a pencil pusher. He facilitated evil for his own material gain and eschewed the personal risks of fighting the good fight, but the only person to whom he posed a true mortal threat was Angel. That hardly makes him evil when compared to an ancient warrior God King thing, William the Freakin' Bloody, and his very own Yoda, the CEO of Hell Inc., himself. Of that motley crew, only Gunn comes off with the possibility of smelling rosier, and he's an acknowledged murder as well as the veritable Judas who accidentally sacrificed Fred for his own personal gain. My memory may be at fault here, but I don't remember Lindsey ever actually directly killing anyone. The only thing Lindsey is guilty of is backing the horse he thought would win and of harboring a vendetta (unfulfilled as it was) against Angel.
One might even argue that Lindsey had a pretty decent beef with the man who cut off his hand, impregnated the woman he loved, took over the very evil company that he fought/punished Lindsey for working for to begin with, turned him over to the powers for that special suburban Hell, and then betrayed him at the last minute by refusing to even fight him directly. In the principled, honor-bound world of the Buffyverse, a fair fight was most certainly called for. Whatever his intentions or future actions may have been, Lindsey should have been permitted to actually do wrong before being executed by Angel and co., who really had no room to judge. And even then, he should have been dispatched in a fair fight rather than an underhanded execution. Lindsey had some legitimate grievances against Angel, grievances that he should have been allowed to air in the good old fashioned Buffyverse way (a big, climactic fight). He also should have been offered redemption, and offered it more than once, like Faith and the myriad of other Buffyverse characters who are or have been morally ambiguous or even downright evil before attempting redemption.
Ultimately, I think Lindsey's death was wrong just like the lawyer massacre was wrong -- these people died to gratify Angel's vengeance, convenience, and other weaknesses.