I had the same problem, and found the solution on MacRumours, posted by one "falkas", to whom all credit is due. I tried it, and it worked first time, like a charm.
It is possible to use the Windows 7 ISO with both x86 and x64 on the same install file. Bootcamp 5 will see this as a x86 install file though and won't allow it to continue. To fix this just follow these steps.
1. Open a Finder window.
2. Navigate to Applications>Utilities
3. Control Click or Right Click on Boot Camp Assistant and select "Show Package Contents"
4. Open the Contents folder
5. Drag the file "info.plist" to your desktop (I also recommend saving it in another place as well in case you want to revert to the original)
6. Open info.plist on your desktop with a text editor
7. Find the field labeled as below:
<key>32BitSupportedModels</key>
<array>
<string>MacBook7,1</string>
<string>MacBookAir5,2</string>
<string>MacBookPro10,1</string>
<string>MacPro5,1</string>
<string>Macmini5,3</string>
<string>iMac12,2</string>
</array>
8. Time to find what your Mac is. Click the Apple in the top left hand corner and select About This Mac
-Click More Info...
-Click System Report...
-Under Hardware Overview, look for Model Identifier and copy it
9. With your Mac's Identifier copied, go back to your open info.plist file create a string at the TOP of the entries. So if your Mac identifier was "iMac13,2" then it would look like this:
<key>32BitSupportedModels</key>
<array>
<string>iMac13,2</string>
<string>MacBook7,1</string>
<string>MacBookAir5,2</string>
<string>MacBookPro10,1</string>
<string>MacPro5,1</string>
<string>Macmini5,3</string>
<string>iMac12,2</string>
</array>
10. Save and close info.plist. Drag info.plist back into the Contents folder and select replace. (You may have to authenticate and enter your admin password).
11. Start Bootcamp and it should allow you to use your Disk/USB with both versions. I wouldn't recommend installing the x86 (32 bit) version of Windows 7, but this will allow you to get to the point of the installation to select x64 (64 bit) if you have an ISO file with both 32 bit and 64 bit combined. Hope this helps.