Amazon does offer Windows Server 2003 R2 in EBS - it is just not 'on display'. Look under the community AMIs, and filter by Amazon Images. The following come up when I search (all are EBS backed and 'official' Amazon images):
ami-0391476a - amazon/Windows-2003R2-i386-Base-2012.01.12
ami-0791476e - amazon/Windows-2003R2-SqlExpress-2012.01.12
ami-0b8b5d62 - amazon/Windows-2003R2-SqlStandard-2012.01.12
ami-1f914776 - amazon/Windows-2003R2-Base-2012.01.12
ami-31914758 - amazon/Windows-2003R2-i386-SqlExpress-2012.01.12
ami-35f5235c - amazon/Windows-2003R2-i386-BaseMultiLang-2012.01.12
ami-49f12720 - amazon/Windows-2003R2-SQLStandardMultiLang-2012.01.12
ami-4bf52322 - amazon/Windows-2003R2-SQLExpressMultiLang-2012.01.12
ami-c5f721ac - amazon/Windows-2003R2-i386-SQLExpressMultiLang-2012.01.12
ami-e5f5238c - amazon/Windows-2003R2-BaseMultiLang-2012.01.12
Slightly more elegantly, you can use ec2-describe-instances to get the same result (I am using i386, because of your comment, above):
ec2-describe-images --filter "is-public=true" --filter "architecture=i386" --filter "platform=windows" --filter "image-type=machine" --filter "root-device-type=ebs" --owner "amazon"
IMAGE ami-0391476a amazon/Windows-2003R2-i386-Base-2012.01.12 amazon available public i386 machine windows ebs hvm xen BLOCKDEVICEMAPPING /dev/sda1 snap-02fc9c66 20
IMAGE ami-35f5235c amazon/Windows-2003R2-i386-BaseMultiLang-2012.01.12 amazon available public i386 machine windows ebs hvm xen BLOCKDEVICEMAPPING /dev/sda1 snap-80463ee4 20
IMAGE ami-31914758 amazon/Windows-2003R2-i386-SqlExpress-2012.01.12 amazon available public i386 machine windows ebs hvm xen BLOCKDEVICEMAPPING /dev/sda1 snap-9ee787fa 20
IMAGE ami-c5f721ac amazon/Windows-2003R2-i386-SQLExpressMultiLang-2012.01.12 amazon available public i386 machine windows ebs hvm xen BLOCKDEVICEMAPPING /dev/sda1 snap-4c7a0228 20
(The above returns both Windows 2003 and 2008 - so either grep, or select by hand - obviously the difference between the two result sets is because the latter is limited to i386 only. The above command does appear to need a key and certificate to run).