Yes, you can enable protected mode on trunk ports
Configuring Protected Ports
Some applications require that no traffic be forwarded between ports on the same switch so that one neighbor does not see the traffic generated by another neighbor. In such an environment, the use of protected ports ensures that there is no exchange of unicast, broadcast, or multicast traffic between these ports on the switch.
Protected ports have these features:
•A protected port does not forward any traffic (unicast, multicast, or broadcast) to any other port that is also a protected port. Data traffic cannot be forwarded between protected ports at Layer 2; only control traffic, such as PIM packets, is forwarded because these packets are processed by the CPU and forwarded in software. All data traffic passing between protected ports must be forwarded through a Layer 3 device.
•Forwarding behavior between a protected port and a nonprotected port proceeds as usual.
•Protected ports are supported on 802.1Q trunks.
link:
http://www.cisco.com/en/US/docs/switches/lan/catalyst2950/software/release/12.1_20_ea2/configuration/guide/swtrafc.html#wp1158863
HTH