There is a weather theme fix on installer.
If you cant find it... you hvae to do it the old school way...
1. SSH your iphone and go to /Application/Weather.app/
2. copy Info.plist to your desktop
3. go to this link
Binary to XML converter
4. Click browes on their website and locate your info.plist
5. Click convert and save your file
6. Open the converted info.plist in notepad
7. locate and delete SBIconClass SBWeatherApplicationIcon
8. paste back the info.plist in your /Application/Weather.app/ folder
Optional:
9. you can delete the other icon that is in /system/library/coreservices/springboard.app/, the file name is SBWeatherCelsius.png
Your all good, now your icon will change along with the summerboard themes.