I've always thouvht that although the original 2003 Clone Wars cartoon wasn't "officially" canon that because the actual canon material never conflicted that we could still regard it aa actually happening. Did the later cartoons contradict the original series at all? I would think Filoni would have a bit of reverence for the cartoon considering how amazing it is.
There were some minor contradictions but regardless, I think the Lucasfilm position now is that the old EU elements are not-canon until made canon and not the other way around.