I dont believe it will have any adverse affect on sharepoint, in the sharepoint settings, you just enter the listener name instead of the actual server name. When failover occurs, sharepoint shouldnt be any the wiser as it is now abstracted from the physical sql server.
make sure youre aware of the licensing requirements with Always On and also if your in synchronous or async commit mode. synchronous can sometimes be a small performance hit which is remedied by async mode at the expense of potential data loss. As sharepoint is a "black box", i.e. you dont really know what its writing to the database at any given time, there is risk that if any critical system data is lost the instance will be damaged.