When could we use gradient ion-pairing separations? As we know it is not recommended due to slow equilibration of ion-pairing reagent on the column which creates an inherently unstable system.

Here is the example of gradient ion-pairing procedure from pharmacopoeia:
...as mobile phase at a flow rate of 2 ml/min a mixture of 0.5 volumes of acetonitrile R and 9.5 volumes of a 3.4 g/l solution of tetrabutylammonium hydrogen sulphate R changing by linear-gradient elution to a mixture of 5 volumes of acetonitrile R and 5 volumes of a 3.4 g/l solution of tetrabutylammonium hydrogen sulphate R over 10 min, followed by the final elution mixture for 5 min,... (BP2002)

We have line of columns with ion-pairing reagent imbedded on the surface of silica gel. You can use any gradient and equilibration time is going to be very short.
http://www.allsep.com/Technology_RetentionOfPolarCompounds.php
You can request brochure from us with the detailed description
mail@allsep.com

I generally do not recommend gradient ion-pair methods, but you can get reproducible results if you use a fixed pre-run equilibration and are willing to throw away the first two or three runs every time you do the assay. Unfortunately, this detail is usually not provided in methods in the pharmacopoeia.