I have two suggestions. Unfortunately, both options involve spending a fair amount of money.
First I want to mention that I do not recommend trying to take your guitar if you are only using panniers.
My first suggestion, involves the purchase of a new guitar case - a
Calton case to be specific. These are very expensive and our custom made to fit your guitar. They are water tight, fire retardent and simply the absolute best protection for any instrument. A case like this would all but guarantee the saftey of your guitar.
My second suggestion, which someone else already brought up, is to add an
Xtracycle to your bike. This is a pretty great system for carrying, among other things, oblong and bulky objects. Combining this set up, with a Calton case would be, IMO, the absolute best solution *speaking strictly in terms of the saftey of your instrument*.
I have not toured with the aforementioned set up but I do use it it the city in all conditions with excellent results.
If cost is really an issue, I suggest a BOB, or similar trailer, and a decent hard case. Buy some foam sheets or blocks and cut them for the inside of yor case to absorb shock and prevent movement in side the case. Pack your tailer and lash your guitar to the top of yout load. A tarp over the top will keep it dry.
If that's still too much, remember that Woddy Guthrie, among others, used to ride the trains without even a case for his guitar!
Finally, I would always suggest against traveling with a guitar which holds sentimental value for you.