IM midazolam should work fine for seizures once it is absorbed, but keep in mind that you are looking at 10-15 minutes for full effect via the IM route. If giving IM, I would increase the IV dose by 50% to compensate somewhat for the slower absorption. In a seizure, it is probably much better to place an IO and give an IV dose.
I have no experience with IN midazolam. In theory it works well, but I hear that patients often snort it out before it is absorbed.
Curious why IN versed was given for intubation, rather than IV? Also, 5mg is a very small dose for intubation. The normal intubating dose is 0.1 - 0.3 mg/kg, and even at that dose it doesn't work as well as other sedatives, which is why you don't see it used as much for intubation as other drugs. I would not expect to see anything approaching adequate RSI sedation in an adult with only 5mg, so it sounds like the lack of effect that you observed there could have been simply due to underdosing.