Honestly, in game solutions for out of game problems will not work in my opinion. If the rest of your table wants the player gone, he needs to go. Either that or you are likely staring at the slow death of your table. However, if you don't want to boot him directly, there are some steps that others have suggested that I would agree with.
1) Audit his character. What is described is not possible to create on the rules as written at 400BP. If it is an error, have the player correct it.
2) Rural area runs will expose a one dimensional character. Lagos and Chicago, both featured in Dawn of the Artifacts will work wonders.
3) Swarms of self replicating IC is a solid way of overwhelming him.
All that being said, does that really solve the problem, the character is dealt with, but based on the situation the player, not the character seems to be the problem. I understand that this player may be a friend, but what about the other players? They are likely friends too. It sucks to have to deal with situations like this, but ultimately it is your table, and if one player is impacting your fun and the fun of the rest of the table, then ultimately they need to go.
The in game "solution" will likely have a number of effects, many of which are previously mentioned:
1) If you smoke the "uber powerful" technomancer in the matrix, it will likely scare the hell out of the rest of your players for matrix ops.
2) The GM fiat that you want to create will likely show your players that such a fiat, a no win situation for a player can occur, and that can shake their faith in your ability to be a fair GM.
3) The player is going to feel cheated or cheesed. And honestly he should. You are asking to have help creating a node that will smoke him. Not an uber secure node that would be tough to beat, but a node to smoke him. If you are not wanting to give him a chance, why bother with the mechanics at all. Deal with it out of game and boot him.
4) The process of smoking him will take time, time that could be better spent on the players that ultimately will be remaining at your table.
5) Building a better deathtrap to kill his character is just going to reinforce the belief he has about cheating, and will do so in front of the other players, once again impacting their view of you as a GM/friend.
You comment that the player is/was a friend. Its kinder to be clear and remove the problem from the game directly rather than indirectly. Honestly, deal with the situation out of game rather than in game. It will be far less messy as if you deal with it in game you will still have to deal with all of the out of game problems eventually.