I don't think that's going to be feasible. Capturing a machine intact is way more harder than blasting it and picking up the pieces. You also run the risk of it escaping during transport or infecting any computer you plug them into.How would capturing mintact achines work mechanically? Could we simply make it a standing order for any combat unit (including mercenaries?) fighting machines to try for capture if there is only one or two left and they think they can get them with little to no risk?
Also, their code is probably so mangled with bugs and viruses that it's going to be easier to just start from scratch.