It is highly unlikely that you will be able to secure mortgage financing with a temporary CO...unless you purchase with a FHA 203K loan. An exception MIGHT be made for a escrow holdback, which would require you, or the seller, to set aside 1.5% of the estimated repairs with your closing agent. A hold back is also set for a specific period of time, usually 30 days.
Very few lenders will approve a escrow holdback in today's market, so that is probably not going to be an option. However, the one exception may be repairs that cannot be made due to weather conditions; such as a roof repair in New York in December (LOL!). If there is any possibility that you will need mortgage financing, I would make sure you discuss your question with your mortgage professional prior to making any offers on the property.