This is tricky. I'm actually kind of fond of the Monster Manual's suggestion of the PC becoming a DM controlled character if they embrace the curse (at least until it is lifted). Since that's not your original question, let's actually dig around and see if we can't get an answer.
My initial assement is that we need to re-examine the rules presented in the Monster Manual for Lycanthropes. If you'll open your hymnals to page 207, we'll see the green box labelled "Player Characters as Lycanthropes" on it.
The first paragraph reads:
The character gains the lycanthrope's speeds in nonhuman form, damage immunities, traits, and actions that don't involve equipment. The character is proficient with the Lycanthrope's natural attacks, such as its bite or claws, which deal damage as shown in the lycanthrope's statistics. The character can't speak while in animal form.
This actually sounds familiar. If you flip back to the Druid in the Player's Handbook and look up Wildshape, you'll notice that the wording is exactly the same as the Wildshape ability, meaning if we're not embracing the curse, and thereby mastering the shapeshifting, we only have to worry about encounters on the full moon getting adjusted.
So, gut answer says "Nah, you're good." However, let's pretend we're normal PCs and go "Sweet, shapeshift!" and embrace it.
As stated earlier, you do entirely have the option (which I suggest!) of taking control of the alignment-shifted PC until they're healed. That'll solve the problem outright.
However, since we're going to begrudgingly get into mechanics, a Lycanthrope in shifted form (based off a human) runs about 3.5 CR, all told. You can add in their class levels, and we'll call it probably a 5.5 CR when they're shifted (I'm assuming level 2 PCs). So, you're definitely in need of some bump.
This sort of thing is a delicate balancing act in a home game, but your goal is to start tuning your encounters to their level. Go ahead and build each encounter as normal, but count the infected PCs as one step higher than the intended difficulty of the encounter. For example, if your party is 4 level 2s and two have lycanthropy, build the encounter at 500 XP budget — 200 for the uninfected PCs, and 300 for the two infected PCs (150 xp/character is 'hard' for level 2) — and run the encounter. Keep about 100 XP or so of monsters in reserve (this will kick it to Deadly) to show up if things are too easy, but be ready to reduce things the same way (−2 AC from all monsters or −5hp is what you'll need to get the encounter on-the-fly adjusted to dial back the pressure).
You'll need to run a few encounters like this to start tuning the difficulty, and I would recommend as well pushing on the infected PCs' ability to control themselves. Wererats are notoriously klepto, at least in my games, as well as nasty, dirty little creatures. There's a certain point at which they'll get disadvantage on Charisma checks, and another where I think it'd be okay to start disadvantaging their wisdom saves as well if they try to resist what is now their nature.
Don't forget too that people don't like Lycanthropes. There's grave consequences — usually wererat/wolf/what-have-you hunters — who will be looking to find the wererats skulking around town. The PCs are also probably a bit unsettling to be around while they're cursed as well, but those are just secondary thoughts for flavor.