If Timo needs to skip qualifying to be well enough to race, then he needs to skip qualifying. Also, if he's not well enough to do qualifying, skipping would still be the right move, regardless of what happened on race day. All the examples DC cited when justifying his position were people who were sick on race day. Well, sorry DC, but there are no points for qualifying and there are points for the race. It's more important to be well on Sunday than Saturday...
Timo has been given the dispensation to race, subject to medical clearance. His time in FP3, while not to his usual standard, was in the 107% margin. If Narian Karthikeyan can get into the Spanish Grand Prix that way, then Timo was bound to get provisional permission.
Yes, it's daft that Marussia's test driver lacks a superlicence. Hint: this is why most teams don't recruit a lead tester purely for money and headlines...