Can we delete records in share table with row cause as Rule?

As per the http://www.salesforce.com/us/developer/docs/apexcode/Content/apex_bulk_sharing_understanding.htm

it is not possible. “All implicit sharing added by Force.com managed sharing cannot be altered directly using the Salesforce user interface, SOAP API, or Apex”

Howsoever, the work-around is this:

You need to change the Sharing Rule which is causing the share. which is to delete a record with Sharing type Rule

If(Trigger.IsUpdate){
List<OpportunityShare > sharesToDelete = [Select o.UserOrGroupId, o.RowCause, o.OpportunityId, o.OpportunityAccessLevel, o.Id From OpportunityShare 
where RowCause=:Schema.RowCause.Your_Sharing_Rule__Here and o.OpportunityId='######'];
}

And then do this:

if (!sharesToDelete.isEmpty()) {
delete sharesToDelete;
}