You should be able to find a suitable combination for a MetaBones adapter and any Canon lens you would like to use underwater among Nauticam's various solutions / port extensions (they mention the MetaBones adapter and Canon lenses explicitly on their website). Phil Rudin (poster here and on Wetpixel.com) should be able to help out if the Nauticam website doesn't provide the answers you're looking for.
There are a few considerations to make. I switched from a Canon 5DII and a variety of L lenses (mostly the F/4.0 zooms, plus a variety of L primes) to a micro-four thirds system and then added Sony's A7r when it came out later, precisely because I mostly photograph while travelling, and the weight was a big issue for me. One thing to consider is that your overall system size will only shrink marginally if you keep the Canon glass and 'only' upgrade the body, although the housing for the 5D is quite a bit chunkier.
On the Mirrorless end of things, if you shoot anything requiring continuous AF / action, your DSLR is still going to be much, much better. I don't, so I'm thrilled with the A7r in most ways, and the mk II (which is a little out of my price range for now) fixes almost every annoyance I have with the original, save the persistent lack of a touchscreen (AF point selection is annoying) which is a non-issue for underwater use. The files are gorgeous, and I'm a big fan of the 55/1.8 and 16-35/4.0 native lenses. No way in hell I'm going back to a DSLR.
Having said all that, my choice for underwater housing is...a sony RX100. Why? because kitting out a full frame camera was too expensive for me, and an RX100 in an aluminum housing, with good (second hand) wet lenses from Inon can be had for a fraction of the cost (like 20%-25%, give or take), with the major advantage that it is a much, much smaller package to travel with. I also only dive when travelling, really, so if I live somewhere where I dived my camera semi-regularly, I might have different priorities.
Buying new, an A7R mk II housing with ports and extensions for an ultra wide lens costs about 6,000 USD. Add at least a strobe an arms (say minimum 500-700, more like 1000 for a larger strobe, or double that for a pair of strobes) and things get very pricey. My idea A7R setup would actually probably be the Sony 28/2.0, and the Nauticam wet lenses (WWL-1 and CMC), which would be a package costing 8,500 dollars, but allowing wide-angle and macro on a single dive using high-quality wet lenses.