I'm not sure if this question is asking a general historical question, or if the question is asking for an answer about Isabel.  I'll go a little bit through both.  

If New York remains in Loyalist control, then Britain has a strategic stronghold.  New York is prime military ground.  It has access to Patriot forces over land, it has a good harbor for the British Navy, and it already has defenses in place.  Additionally, because it's a big city, it has plenty of places to house British troops.  If New York stays Loyalist, many Patriots will vacate the city.  That will open up room for British forces.  

For Isabel, if New York stays under Loyalist control, she isn't likely to get free of Madam Lockton.  The Locktons are Loyalists, so if New York stays friendly to Loyalists, the Locktons have no reason to leave.  If New York were to be taken over by Patriot forces, Isabel stands a bit better of a chance at escape and/or freedom.