I do think malware needs to be significantly toned down however, I (and others) don't think it's right that months and months worth of work can be taken out in 1 hour... But I can't really think of a way to change it without just making it rubbishly weak. Possibly increase AP cost to 20 each, but people can still and do still overclock their AP from faction missions to tens of thousands.
Maybe a way to tone down the malware is to increase the AP cost in proportion to the amount of time it's been charging...maybe after a week or so of charging up start increasing AP cost by 10 AP each day after the set time. So say you have your silo of malware ready to strike down terror and it's been charging up for 4 months each virii would cost 1200 AP to fire.