I don't think there is a non-NTR run?
Even if you pay all your debts, never let the girls cook with the guy--- They still become sex-crazed with the Uncle.
If anyone knows a way, let me know, or is that only for New Game+
You can avoid Roy by having whichever girl you confess to and become "lovers" with cook with Roy (and never the other girl). He won't gain favor cooking with your girl and won't date the girl either. Keep in mind the other girl is still avaiable to date even if you avoid cooking so it's a ticking time bomb especially because if he has sex with her it essentially unlocks Tommy too.
You can avoid Leonard by paying off debts. Simple!
You can avoid Tommy by keeping the girls away from having sex with anyone but you. Note that ending the game with them as virgins seems to count as a Tommy ending so you still have to do some work.
You can avoid normal customers by just not letting their lust cap(999) during the day and not having them do sex service. You can have them do touch, undress and blowjob however at higher ranks even these will turn into sex so once you get generic girls have them take over, less money but keeps your girls safe.
You can avoid the noble's minigame by save scumming... no real way around it.
All this comes together to basically this:
You need minimize cooking with roy early and restrict what small cooking you do to the girl that will be your "lover". This means sticking largely to serving drinks and H services. This can be a problem early on because you also need enough money to pay off Leonard. Focus your skill selection on increasing the likelihood of H orders and more customers (and generic girls to help do the H services). Do not get food skills until you get that "lover" status. Once you get to "lover" status with one of the girls she is safe from Roy so as long as you stayed below 475(I think? might be 500) favor he won't have sex with her. Since you're the only one that will be able to have sex with her at that point unless you specific ignore her lust, fail the noble mini game, fail to pay debt, or specifically tell her to have sex with a customer she is safe for the rest of the game and you can come back to her whenever.
You are in a race against time for your non-lover girl though. Every time Roy takes a girl for a date he'll only have the option to take that girl and if the favor hits 475 and he has sex with her it also unlocks Tommy's ability to have sex with her and he will go after her constantly (like nearly every damn day) him along with Roy both going at her night and day make it difficult for you to even get opportunities let alone succeed in getting her pregnant. Making sure she does some H orders (touch, undress and blowjob A rank or below) gets her lust up and makes it easier to have sex with her often and you'll need it. The chances to get the non-lover girl pregnant seem to be super small (like 1-2%). You could probably just save scum your first time with her if you really want. Typically I find(at least on simple difficulty) it takes like 5-6 weeks before Roy gets to 475 and shit hits the wall though so it's not like you have no time at all. Once you get her pregnant you can work on your "lover" girl at your leisure since she's safe.
Once done huzzah! you win! except there is no ending for getting both girls at the same time for you... you just get 2 endings for each individual girl unlike Roy, Tommy or Leonard who all have special endings for getting both.
Or you could just blow through the game not caring complete it and do a new game and use the cheats. Up to you.