I think that Tom's biggest flaw was his need for approval and love from his adopted family. The book delves into this a bit more, even describing a recurring nightmare that Hagen has of being homeless and blind, and his only comfort is waking up in Vito's house. This leads to a unquestioned loyalty to his adopted family and a need for their love and approval. Perhaps this stopped him from being too ruthless, perhaps it stopped him from being truly forceful in his advice to Sonny, Vito and Michael. If this same need drove him as a Don, then he would be a weak one.
If Tom believes that the only thing keeping him safe and warm is Vito's succor then I would think, yes, that he would be very loyal. But I also think that would make him all the more ruthless when that source of comfort is threatened.
Also, he seemed pretty forceful with Sonny. He yells at him on several occasions and successfully gets him to change his mind about killing Sollozzo (until Michael speaks up). I can't imagine Genco yelling at Vito, or dissuading him from a course of action.
Tom certainly favored negotiation to an extreme, but I'm not sure it's because of the reasons you state.
I wonder if Vito recognized Sonny's temper issues and consiously molded Tom into an overly conciliatory man as a counter-balance.
