As mentioned above, you will probably have some metal shavings in the diff fluid. This is normal. It's highly unlikely that your differentials are messed up.
As for $4k to change the rear, they are out to lunch!!!!! Whatta bunch of rip off artists!!! I sold a perfectly good Explorer rear axle complete for $150 US. That included the gears, axle and brakes. It takes about 2 hours to install a complete rear axle assembly if you know what you are doing, so if the rear differential was actually bad, you can get a used one from the junkyard, and have it installed for under $500 total.
THEY ARE TRYING TO RIP YOU OFF!!!!!!!!!!!!!! If you feel you need to, change the fluids like you mentioned, get the slip joint lubed, and you will be fine. I had a '92 Explorer before I bought my new one, and I had never changed the axle or transfer case fluids, and they were fine when the truck got totalled at 105,000 miles. I had offroaded it and I drive my vehicles hard.