I know someone here mentioned that you could possibly remove the left side cover by flexing it (severely). I got to thinking, if this happened to me (flat bike battery and the mechanical key didn't work), I think I'd have a go at busting out the side cover so I could jump/charge the battery.
I did a quick estimate of the costs involved...
Left Saddlebag parts as a result of hole saw drilling...
LID SET, L. SADDLEBAG (TYPE1) (WL)
81420-MKC-A30ZA $694.66
INNER LID, L. SADDLEBAG
81441-MKC-A00 $201.07
RUBBER, SADDLEBAG LID SEAL
81350-MKC-A00 $41.78
Total $937.50 plus a heap of labor
Left side cover parts (inner and outer)...
COVER A, L. SIDE (TYPE1)
83710-MKC-A00ZE $77.63
COVER B, L. SIDE
83712-MKC-A00
$106.30
Total $183.93 virtually no labor
Of course if it is some electrical failure other than the battery, I guess you're in trouble. In that case I'd start by going underneath and using pliers or a die grinder to remove the three philips head retaining screws and removing the hinge pins. That might not get you fully open but I'd try anything before the hole saw.
Anyway, what's done is done and I hope the OP gets it fixed soon.
As mentioned before, everyone should check their emergency key actually works. Many bikes need the rod in the latch mechanism adjusted slightly to ensure it fully releases the front catch. It's an easy job while you can get in there using the electrics.