Dont know if its the same for the SL but i rememeber reaidng a post where a guy found a point in his CLK where he could attach a battery booster pack so that he could open his boot again to get at the battery (i'll try find the post)
the point was in the passenger side footwell you will have to lift the carpet.
Its possible that you're using a service key to manually unlock as opposed to the master key. The boot is designed to be manually unlocked in the event of power absence. Did you buy your car with ALL the keys ??
I had a similar issue on a 202 c class (barrel broken and flat battery). Luckily for me, the barrel was able to be slid out due to the housing being broken - this makes it quite easy to open the boot via the mechanism that's behind the barrel of the lock. (A mobile mechanic opened the boot with a screwdriver in roughly 20 seconds).
It's possible it might be cheaper for you to try and remove the barrel from the housing than destroying any firewalls/rear light clusters. But check with a garage about the cost of replacement parts first!
OK - the AA man plugged his booster into the cigarette lighter and this powered the vacuum enough to open the boot. The lucky part is that he didn't blow out a bunch of other electronics!