It is quite plain that 'direct', in this context, means addressing the harm head on.
Cf. Webster's (1913):
1. Straight; not crooked, oblique, or circuitous; leading by the short or shortest way to a point or end; as, a direct line; direct means.
2. Straightforward; not of crooked ways, or swerving from truth and openness; sincere; outspoken.
3. Immediate; express; plain; unambiguous.
Obviously, this will entail a face-to-face meeting on many occasions.
However, there are other principles involves in Step Nine, namely tact and consideration.
Not everyone appreciates being tackled face to face. Not everyone can be seen face to face. Not everyone has the time to see us face to face. It is not necessarily tactful or considerate to make an amend face to face and effectively force a response on the spot: people often feel compelled to respond verbally then and there and sometimes say either rash or insincere things. Some recipients are so irascible and reactive that any attempt to have a rational, reasonable conversation will immediately descend into something quite different, and it can be impossible to get the message across in person. Not every burgled person particularly relishes the prospect of the 6'3" brick-out-house burgler darkening their doorstep with a mawkish apology. Sometimes a physical reappearance can reignite old romantic wounds in a way that a letter would not, and the amend can be eclipsed by the resuscitation of old emotions that are best left undisturbed.
In short, there are many circumstances in which a phone call or a letter, either by way of first approach or as the mode of the amend itself, is more appropriate and in keeping with the principles of the book.