Your friend will not be able to pass all of the running costs to his business if only 50% of the flying is on business. Instead, he will need to pay his own company back for the personal flying that he does at a commercially tenable rate, and/or risk the possibilty of the flights being treated as a benefit in kind.
An accountant is the person to ask here. They will have the job of preparing the accounts in a way that will keep the dreaded Inland Revenue happy.