Mac OS? If yes, I believe something named "crosspack" takes care of the problem.
Lunux? If yes, I believe you can pick and choose the AVR-GCC version.
I've been tempted to see about switching to avr-gcc and a more traditional make / compile / link process, though. But that feels like a bit more trouble anyway.
It is for me (more trouble than it's worth). I hate fiddling with tools.
I'm not entirely sure what I'd be leaving behind and what I'd be gaining in the process.
For the latest WinAVR version you'd be giving up some bugs. The PCREL bug is the only serious one I've encountered.
For the latest AVR-GCC I believe you'd be gaining C++11.
Were I in your shoes I'd just replace ld