Never create a .DS_Store file again
As Fake Name pointed out, Total Finder comes with a kernel extension to redirect .DS_Store files which effectively prevents those pesky files from being created in your directories and without losing the function. What he/she didn't point out is that the kernel extension can be downloaded without Total Finder from github. You have to build it and drop it in your /System/Library/Extensions directory. Then you should restart your computer. It appears to be working for me so far.

Update: This is now a separate project from TotalFinder called Asepsis. There is now a lot more documentation on how it works and the installation process. The GitHub repo is now located here.