This is how I see it:
Seastone/Sea DOES NOT REMOVE the specific Devil's Fruit ability. It only makes the body of the user weaker and more suspectible to attacks otherwise immune. And if they are in that weakened state, e.g. inside a Seastone net, they cannot move and use their DF powers obviously.
For example, when Luffy was underwater in Arlong arc, his body could still be stretched, but he himself couldn't move.
When Kalifa was in the bath, she could use her bubble-powers from the parts that weren't underwater (arms,head etc.) but not the parts that were underwater.
Now, when a Logia user gets hit with a Seastone-glove, the impact area would give damage to the Logia user, but since it's only a brief connection with Kairouseki, they would be able to use their Logia powers from the other parts of the body.
But if they would be trapped in a Seastone-net, they would gradually become unable to move and use their Devil Fruit powers so you can kick their asses easily.
Basically, the user is just unable to use their Devil Fruit's power in the area it is contacted with the Seastone/Sea but an outside source could make it work (depending on the power).