The low damage phases are a smaller part of your healing than the high damage phases and the added crit does not really help that much considering that the vast majority of your absorbed aegis during low damage phases is from the tanks.
Also consider that absorbs from heals are given by the formula crit*(1+mastery)*(1+0.5*mastery). So mastery also increases the amount of aegis you put out. Lets see how this works out
The rate at which crit rating increases absorbs is (1+mastery)*(1+0.5*mastery). The rate at which mastery increases absorbs is crit*(1.5+mastery)*1.6
So at 25% crit and 28% mastery the rate at which crit increases absorbs is 1.28*1.14 = 1.4592. The rate at which mastery increases absorbs is 0.25*(1.5+0.28)*1.6 =0.712
Thus mastery increases absorbs at roughly half the rate at which crit increases absorbs, however you also forget that PWS is a significant part of your absorbs during low damage phases. The rate at which mastery increases PWS is (1+crit)*1.6, while the rate at which crit increases PWS is (1+mastery). Using the same values as above you get 1.25*1.6 = 2 for mastery and 1.28 for crit.
So if 30% of your healing during a low damage phase is PWS, 50% is aegis and 3% is your non overhealing heals the rate at which mastery increases your healing would be 2*0.3+0.712*0.5+0.5*0.03 = 0.971, while the rate at which crit increases your healing is 1.28*+1.4592*0.5 = 0.933888
Surprised? You should be. Mastery is nowhere near as bad as you think during low damage phases.
Lets say you cast 1.5 penance, 5 smites and 1.5 holy fires per PWS. Then the amount of raw healing done by atonement is about 4 times that of PWS. With 25% crit rate and 28% mastery that means aegis will be equal to 1.28 of a PWS, so the values I picked for my example are pretty reasonable. I cast twice as much PWS during low damage phases though.
Basically crit has little benefit for low damage phases over mastery because PWS is an important source of heals and both crit and mastery increase both aegis and pws, but with opposite effectiveness.
Balanced mastery crit is always better than full crit and full mastery no matter what. The balance point is dependent on your casting pattern and healing style, but typically it lies somewhere between the balance point for heals and for PWS.