don't have time at the moment to get into details, but I'll give you my quick answer from my experience... machined parts are always a concern for long term applications in which fatigue cycling is a major factor (few environments more severe than helicopter structure)... cold working the surface (normally a peening operation) can help regain some of the fatigue life by closing off the grain boundaries opened by machining and inducing pre-stress into the surface...
basically, without knowing more about the specific application you are working toward, I don't want to go too far with recommendations... what I can say is that we use machined parts, even in extremely critical fatigue environments of fighter A/C... if you make a good material choice, take care to control the macro concerns (generous radii, avoid abrupt cross section changes, good surface finish), and use some technique to cold work the surface - I feel you can use a machined part in most applications...
all that being said, despite very careful process controls, etc - we still lose machined parts due to fatigue related failures, but in several cases they have performed better overall than the composite components they replaced...
if you do go with a machined repair, I recommend adding an appropriate inspection interval for the repair... you are obviously repairing some damage currently - which means you had some sort of noticeable failure without the loss of the helicopter - hopefully that means any future problems in this area will evidence themselves before something catastrophic...