I read in one of the forum that it may create a problem if I allow native vlan through the trunk port connecting two switch.
But I am still not getting exact consquences of doing so?
You need to decide whether you want to route or switch between the 2 pairs of switches.
What i would do with the information you have given so far is to connect A -> C and A -> D, B -> C, B -> D with L2 trunk links.
A & B would not have a trunk link between them but C & D would be interconnected via a L2 trunk.
Then migrate the L3 interfaces + HSRP configuration off A&B and move it on C&D. So A&B are not routing for any vlans any more they are simply access switches connecting back via L2 trunks to C&D.
This would give you a more standard setup.
Alaternatively you can leave the link between A&B and leave it routing for vlan 125 etc. and make the links back to C&D L3 routed links. And then run EIGRP between all the switches. Note that with CatOS you cannot actually have a L3 routed port ie. "no switchport". What you do is use a /30 subnet and create an SVI on each switch eg.
int vlan 200
description L3 connection to C
ip address 192.168.5.1 255.255.255.252
int vlan 200
description L3 connection to A
ip address 192.168.5.2 255.255.255.252
and then assign the port on A & C into vlan 200. Then repeat with a different subnet for
A -> D
B -> C
B -> D
Each has their advantages and disadvantages. If your switches are all running CatOS i would use the first option of L2 trunk uplinks and migration of L3 interfaces off A&B to C&D.