Such is the age old practice in the Church and is key. The regular confessor may need to direct a penitent even on the matter of confession -but such is still key.
The regular confessor can guide them. Direct them
A regular confessor can guide them. The person with scruples needs such…whatever concern that can be raised the answer will be the same. Such is key.
Some scrupulosity can be a lack of formation. Sure. Such often is cleared up rather quickly.
There can be “transient scruples” such as in the case of new converts or those who have had a deeper conversion. Again such can be more quickly cleared up.
Otherwise scrupulosity can be of various kinds and degrees and I imagine various causes (biological etc)- in some cases a person with OCD for example with be scrupulous as well. As you noted Canonized Saints who where quite well formed - or even masters of Moral Theology -struggled with scruples. The very patron of Moral Theologians for one! Priests and religious can struggle with such as well as rather formed lay persons.
In any cause a kind of “obedience” to a regular confessor who knows of ones scruples and can direct one is the age old practice. Also sound Catholic Counseling may be in order in some cases or medical intervention (such as cases of OCD).