Both are correct.
It's an instance where there are only slight differences among the constructions and where interpretation of the nuances may well differ.
The first option is:
the guidelines suggest a confirmed diagnosis before initiation of the treatment
which implies any initiation of treatment, that a specific treatment is recommended and is written (without the first the) in a tighter style, more likely to be used by the medical profession;
Your second suggestion:
the guidelines suggest a confirmed diagnosis before the initiation of the treatment.
is just more fully written out and suggests that a start for the treatment is already in prospect; it also suggests that a specific treatment is recommended.
but there is no difference in meaning.
The other option, which you have not suggested, is:
the guidelines suggest (a) confirmed diagnosis before initiation of treatment.
omitting both uses of the, which sounds more like typical medical shorthand and leaves open which treatment might be recommended.