I have a 2004 RM 250 and have had to replace my steering stem bearings. They, too, were rusted out. I replaced them with Pivot Works - top and bottom bearings and races. I did that in January after one year (I greased them when I bought the bike and six months later, too). I just checked them again a few weeks ago and they were showing signs of rust again. I decided to use the thick Bel Ray grease instead of the lighter Torco grease I was using.
If I remember, my Honda had a 'cover' over the top of the bearings. I looked up the part, and they call it a dust cover. I'm thinking of seeing if this will work on my Suzuki to keep the water from getting down there. Right now it looks like an easy route for water to make it down. Honda also has a lower dust cover, and I'm thinking of trying one of those, too.
Anyone have any solutions to protect the bearings better? Ditto for the rear - I just had to replace my rear linkage bearings.