I think the "I ruined half her life" didn't refer to him not requiting Martha's feelings, or even things like landing her (inadvertendly, but still) with horrible three months in 1913 - it referred to what the Master did to her family. Remember, the last thing the Doctor remembers of the Jones' - though not Martha - is all of them haunted and devastated after a year of horrors. And that wouldn't have happened if Martha had not been his Companion. Yes, it was the Master's doing, but I can understand why the Doctor would feel responsible.