Hello,
The VTP Pruning feature will not help you, unfortunately. The goal of VTP Pruning is to temporarily block existing unused VLANs on trunks to prevent broadcasts from unnecessarily flooding into parts of network where there is no member of those VLANs. However, the VLANs will not be removed from the VLAN database, but rather only selectively blocked or unblocked on trunk ports. The size of the VLAN database will not be smaller.
Probably the only feasible course of action for you is to move the switch into the VTP Transparent mode as you originally suggested.
Please note that even if a switch does not have any access ports in a VLAN, it must know about those VLANs which are traversing it via trunks. If a frame tagged with VLAN X enters a switch via a trunk, and the VLAN X is not defined on that switch, the frame will be dropped rather than forwarded out some other trunk. Bear this in mind when minimizing the number of VLANs on your switch.
Best regards,
Peter