Mill the material to thickness before waterjet cutting, or press straighten after milling. Any process done to this material will cause some warping.
To mill it in the hardened state try cermets or cermaics.

Is it warping when it is waterjet cut. Or after it is milled?
Some steels release stress when waterjet cut and do not come out true size/shape.
In general I leave 0.5mm on for milling and add lugs to the sides of the part that I then use to clamp it in the mill, 5mm holes in the lugs Then grind them off afterwards.
Some high strength aerospace alloys particularily nimonics need 2mm on then clean up on the mill 0.5mm a pass
Tin coated hss cutters 6mm dia 4000revs 400mm/min feed work great for me

Try double disk (twin disk) grinding the equal removal of stock should solve your problem.

Try an octomill 05 face mill from Seco Tools(carboloy in the States).Use a PVD coated micro grain e.g.F40m in an easy cutting geometrie,with the small depth of cut you can use a higher cutting speed than normal and use lots of coolant.
What works very goed on these types of materials including ordinary stainless is the following.
If you using a face milling cutter from say diameter 80 mm
and it has 6 teeth,take out 5 inserts and leave one in.
This isnt the fastest methode but its a good solution when machining thin products.I use this method when trouble shooting,hope it works for you,If so let me know.Kind regards.

Based on your discription, there appears to be some residual stresses in the material prior to machining.  I am guessing that water jet cutting will not induce many stress, if any, in the material.  I am betting that that material is stressed during the aging treatment.  I am also betting that after you solutioned annealed the material, the part did not stay straight during annealing and was subjected to a straightening operation.  You may want to stress relieve the material prior to milling.  You can stress relieve 17-4 in the H900 condition at 850F max temp for 3-6 hours.  

I have milled quite a bit of this material in the past and
agree with BobUXL, You almost always have to stress relieve
this material in the H900 condition prior to milling.

Once stress relieved, I think you'll find the material to
quite stable and repeatable.