FIrst of all, whenever we see a child with headaches, there are a few things we listen for that are red flags for something potentially serious. One of them is that the headache has woken your child from sleep and another is that the headaches are worsening - both of which you report. Another thing is that migraines do NOT occur daily. There are a number of headache types that this could represent such as basilar migraine or cluster headahce (very rare in kids), but unless I take a full history and exam myself, it would be difficult to try and guess what this is. It's somewhat reassuring that the MRI just shows a cyst and nothing else that really stands out. Although I haven't personally seen your son's MRI, I tend to agree with the neurosurgeon in that it's unlikely that the cyst is causing his symptoms. However, there are other tests that may be considered such as an MRI of the arteries and/or veins in the brain to make sure everything else looks ok and one with contrast. Also, an EEG to help evaluate these fainting spells and possibly some bloodwork may be considered. A neurology examination should be helpful. The behavior changes sounds secondary to the underlying problem which appears to be headache.
As for treatment, some pediatric neurologists feel that abortive medications such as a combination of benadryl (to help him sleep it off) and naprosyn (for the headache) are helpful. Other suggestions include midrin and meclofenamate. Preventive meds such as elavil (usually used for older kids, but if monitored may be used in children and can help elevate mood), inderal, calcium channel blockers, cyproheptadine and methysergide can also be helpful. If the headaches continue to worsem and your son has nausea, vomiting or other neurological deficits, you ma want to bring him back to the ER just to make sure he's ok. Good luck.