As of right now, its a "choose one or the other" situation right now. Same as it is with states that allow for medical marijuana cards. People sometimes forget Hawaii allows medical marijuana cards, because we do not have any dispensaries like other states so it isn't in the public's eye as much.
With a medical card, it is registered in the state, and very easy to cross check to see who has both a medical card and firearms registered under their names. I am not sure if HPD has ever done random crosschecking like this though.
With states like Colorado and Washington, where it is legal and completely unregistered, there is no way to cross check. The only way you are likely to get arrested from marijuana abuse is if caught driving and given a DUI. For any other infractions, like smoking in public, you will just be given a ticket. Remember that it is still illegal to smoke anywhere but private property with permission from the owner.
As for the feds breaking down stoners doors to grab their guns, I don't think it is something that is going to happen on a regular basis. If say, they have suspicions of someone doing something a bit bigger, I'm sure they will use the "weed-gun" excuse to come a knockin.
What I think is going to happen... Marijuana will likely be slowly adopted to being legal state by state, but it will be a long while before it is accepted on a federal level. I don't have a problem with this. Pakalolo is the lowest name on my list of substances which I think are dangerous. At least the state is making more money, I think there is something like a 25% tax, which they think will bring in $70 million a year in Colorado.
For the record, I used to smoke weed. Then I grew up and stopped.