First the good news: you can certainly upgrade to Gradle 1.3 and still use the SFTPResolver in the same way you can in 1.2. Everything that worked in 1.2 should work properly in 1.3.
The bad news is that ivy.xml modification is only available as part of the new ‘ivy-publish’ plugin that was introduced in Gradle 1.3, and the ‘ivy-publish’ plugin does not yet have support for SFTP publishing.
You might be able to get things to work by using the ‘ivy-publish’ plugin to publish to a local directory, and then script something up to copy the publication to the correct location on the server. Not ideal, I know, but it might be a workaround.