Water should not be collecting on the seal (I'm having trouble even envisioning that; the seals don't really have a surface on which anything can collect) or spilling into the vehicle. If it is, the better solution would be to figure out why and address that. Can you post pictures?
As a first step, make sure the seal are attached tightly to the door—they can come loose from their mounting pins, which can block the drains, which can prevent the door from draining properly.
Removing them altogether will net you a noisier, draftier vehicle.
2006 WK Laredo 4x4 4.7L
1993 ZJ Laredo 4x4 4.0L — Dead, sold, and rolling again