Maybe setting two separate X screens up to replace TwinView will solve your problem?
Checkout your xorg.conf file for sections: ServerLayout, Monitor, Device and Screen, mine looks more or less like this:
Section "ServerLayout"
Identifier "Layout0"
Screen 0 "Screen0" 0 0
Screen 1 "Screen1" RightOf "Screen0"
InputDevice "Keyboard0" "CoreKeyboard"
InputDevice "Mouse0" "CorePointer"
Option "Xinerama" "0"
EndSection
Section "Monitor"
Identifier "Monitor0"
VendorName "Unknown"
ModelName "Unknown"
HorizSync 28.0 - 33.0
VertRefresh 43.0 - 72.0
Option "DPMS"
EndSection
Section "Monitor"
Identifier "Monitor1"
VendorName "Unknown"
ModelName "Samsung SyncMaster"
HorizSync 30.0 - 81.0
VertRefresh 56.0 - 75.0
EndSection
Section "Device"
Identifier "Device0"
Driver "nvidia"
VendorName "NVIDIA Corporation"
EndSection
Section "Device"
Identifier "Device1"
Driver "nvidia"
VendorName "NVIDIA Corporation"
BoardName "GeForce GT 520"
BusID "PCI:1:0:0"
Screen 1
EndSection
Section "Screen"
Identifier "Screen0"
Device "Device0"
Monitor "Monitor0"
DefaultDepth 24
SubSection "Display"
Depth 24
EndSubSection
EndSection
Section "Screen"
Identifier "Screen1"
Device "Device1"
Monitor "Monitor1"
DefaultDepth 24
Option "TwinView" "0"
Option "metamodes" "CRT: nvidia-auto-select +0+0"
SubSection "Display"
Depth 24
EndSubSection
EndSection
Then I can set two different screen resolutions for each screen. There are some disadventages of this, like impossibility to move windows from one screen to another, but to avoid them you could try to setup Xinerama.
Well, you gotta try to find out what's the best for you.