When you put a property under contract that is not listed (there is no listing agreement whatsoever) and one that you found from your own marketing efforts, why would your Broker be entitled to a commission?
When you discuss this scenario with your Broker, of course he or she would say they're entitled to a commission. I have personally done deals (non listed properties) and wholesaled it and retailed it and my broker did not get a cut of the commission because there was no commission in the deal. I was dealing directly with the seller not a listing agent.
At closing when I wholesaled the property, I sent an invoice to my title agent and I/my entity was added as an additional payee on the seller side under the HUD-1.
Now when I was retailing the property and I was ready to sell, I listed the property where I was the listing agent and signed a listing agreement with my Brokerage.
If the reason you want to pay your Broker (even if the property is not listed) is to maintain a great working relationship with her, its okay to do that being probably a nice guy. But it is not based on a legal obligation you have with her. Verify with your own attorney to be 100% sure.