We use the Publishing Client Add-on for ArcCatalog for all our BATCH publishing. You just select the folder containing the metadata, and the Client publishes any metadata XML if finds in that folder. It claims to find the metadata attached to Feature classes in geodatabases. With the proper permissions to access the SDE folders I do think it would be possible.
We haven't actually tested that because our corporate datasets in SDE are locked down to read-only for most staff-users. And we have not tried automating publishing with a nightly process. We just select the folder we are ready to publish metadata in, and use the simple GUI provided to publish metadata in batch. It creates a log, which is useful to ensure metadata publishes successfully, but we publish in manageable size allotments to keep track of what doesn't publish, because publishing and validation are tied together.