I don't know of any PCs that have been damaged by accidents with secondary ignition. Have seen a few scopes though...
With reasonable caution, this should not be a concern. First, the secondary leads are designed to blow and shunt this voltage to ground. That's what usually happens, but on rare occasions, the scope channel bites the dust.
Reasonable caution would involve not hooking up the scope to vehicles that you know have bad wires. If you can hear the spark getting out you don't need the scope to find that...Use the water scope

Also, do not push your luck by doing max KV output test with the scope connected. You don't need the scope to do that anyway and there is no reason for the risk.
As for PC choices...
Two schools of thought on that.
1. Get a PC that is tough and will last a long time and withstand a tumble.
2. By a $500 PC that you can get several of for the price of a rugged one. They work just fine and the ruggedized one will be outdated in a couple of years anyway. It may fall and be destroyed by carelessness, but you can just go get another one and be back up and running in a few hours. Most techs are setting up test stations that minimize the risk of a tumble and the inexpensive PCs are working out really well.