Not really an answer, but too long for a comment, and I will point it to the answer if/when I find one... Have spent hours on this today.
The OP approach appears to be obsolete due to this change : https://www.raspberrypi.org/forums/viewtopic.php?t=97314 which means that a large amount of advice on forums about the RTC doesn't apply any more.
I've been able to get 'hwclock' working by enabling I2C and drivers using raspi-config (turn on I2C and drivers, in 'advanced settings') and then add
dtoverlay=i2c-rtc,ds1307 to the bottom of /boot/config.txt
So great, hwclock appears to then work and read and write the clock. But you then need to make changes so that 'fake-hwclock' is removed and replaced by proper reading of the hwclock at startup.
This is a good guide on that - although details for a different RTC. https://www.raspberrypi.org/forums/viewtopic.php?p=842661#p842661
But it doesn't seem to apply to 2015-05-05-raspian-wheezy, the lines to be commented out in /lib/udev/hwclock-set are not there. For me, by the time /etc/rc.local is executed, one of the existing startup scripts has already corrupted the RTC somehow.
This is the kind of issue that conventional forums are really bad for - there's lots of good advice that applied in 2012, and then a long series of ifs and buts and you may collect the updated truth eventually. I can't find a direct question to this issue - how to install an RTC for raspian - on this SE, so I'll ask it, and end up pointing this there.