Do you still get the benefit of having an ally if that person has been killed? They still show up in my ally list and I still have to pay to have them as an ally so I would assume the benefits would still be there, is this correct?
Thanks in advance.

You still pay the upkeep costs even if your ally is dead.

Your dead ally provides zero benefit. None, whatsoever, it is as though you have an empty ally slot (but you still pay the upkeep, and they still show up in the upkeep section of a spy op).

Another question:

Can an ally in protection help to defend you?

Probably, but it won't be of much help.

non-commie 100% turret production and mostly indies and some farms besides cs's gets ~40k-50k turrets depending amount of indies and 25% from that isn't much.