There are a number of ways, I can think of, but perhaps consider a pump (powered[1]) slurping water from one hole to another. Pressure-plate can be linked to floodgate or bridge (to block the slurp or dump) or the input gear to the pump to control. Pressure plates in either slurp or dump holes (depending upon your choice of go/no-go method) give you the opposite sign of trigger to the one sent to this pump.
If it's the dump-hole side you can perhaps add a second counter-triggered pump to slurp out the dump into a drain whilst just ensuring sufficient water at the slurp-hole side to transfer over when needed. If you make it with the second pump returning the fluid in a largely[2] self-contained cycle then you effectively have a split-repeater. In one activation state the fluid is in one hole, in the other state it is in the other.
I think that the following basic plan would work:
###### # : wall/uncut rock
#o>>o# o: channel/no-floor hole into slurp&dump holes
#o<<o# >> <<: counter-directional pumps
#####
...not shown are the fluid-blocking constructions, if used, placed over the holes accordingly.
Though I've never tried the slurp/dump from/to two holes each (I'm just juggling in my mind how I'd block one side with a triggered retracting bridge, etc), so I've used a slightly less less compact four-pump circuit, in the past:
######
#o>>o#
#^##v#
#^##v#
#o<<o#
######
...this can be built to hold a state of filled in two opposite corners upon trigger and the other two opposite corners when untriggered, with appropriate fluid-blockers in like diagonal configurations above the holes, or two of the pumps (opposite sides, either way) being mechanically isolated from the otherwise permanent power-source.
At Z-1, in the holes, you can have a maintenance access door for when that hole is empty, to configure the onward-trigger connections after you get it working (whether you knew which orientation was which, in advance) and even a fluid-(re)fill channel/drain on another vector for major initialisation/deinitialisation purposes.
##+##+##
##D##D##
~F+##+F~
########
########
~F+##+F~
##D##D##
##+##+##
...obviously get levers to the Floodgates, and it might be advisable to lock/lever the Doors. If you're wanting to squash more of these together you can have the doors/drains on the 'inside' of the corners leading to downward access/draining stairwells in the centre-four block and share water-supplies with adjacent units.
((Only suggesting this method as my occasional favourite, of my own age-old design. It has its problems in implementation, certainly might not be the
most efficient fluid NOT-gate, but it strikes me that you'd prefer something with more challenge...
))
There's also
mechanical logic, but you'd need a (probably) power-to-signal converter that likely involves fluid.
Creature logic is more of an art, not a science, but can be fun. I haven't really tried using
minecarts themselves (even the passage of your delivery-minecart to pre-empt any danger?) but maybe you'd be more comfortable with that. If you
want to feel comfortable..!
[1] And can be anywhere on you map, through spooky-trigger-at-a-distance, so could be wind-powered at the surface if you have wind, or water-powered from such natural or water-reactor flows as you can tap into or create.
[2] Beware of evaporation and spill, if not a 'tight' system.