You can use a peristaltic pump with a bag. This pumps water into the bag in a bi-directional way, and requires no valves, as the pumps are self-sealing.
This system is used in Norbert Bruggens 'Delta' and the Thundertiger Neptune.
The disadvantage of these pumps, are that they're rather slow in operation- medium size models tend to pump between 200-400ml per minute, therefore they're better suited to craft with a low freeboard, and small ballast tank requirements.
You would also need power to surface, as the pump has to be run both ways.
Unfortunately, all the ballast systems have pro's and con's. The closest to nirvana IMO is a combination of a compressed air system, coupled with piston tanks for trim, unfortunately it's also the most complex to engineer.