Found the way to get rid of above error. I am posting solution here so that it will help others who are facing same issues. See the script I have created below.

/*Jatin: following trigger is enabled when replication is setup/altered

If it is Enabled then SQL developer will get following error while they try to

Alter any Procedure in database which is in replication.

Msg 21050, Level 16, State 1, Procedure sp_MSmerge_ddldispatcher, Line 12

Only members of the sysadmin fixed server role or db_owner fixed database role can perform this operation. Contact an administrator with sufficient permissions to perform this operation.

Resolution: Disable this database trigger. Since we are not replicating any procedure or functions,

it will not harm if this trigger do not fire.

*/

IF EXISTS (SELECT is_disabled,* FROM sys.triggers

WHERE parent_class_desc = 'DATABASE'

AND name = N'MSmerge_tr_alterschemaonly'

and is_disabled =0 --0 means DB Trigger is ENABLED

)

Begin

DISABLE TRIGGER [MSmerge_tr_alterschemaonly] ON DATABASE

End