First, the party needs to state a goal
"Decide to parley" is not an action the party is attempting, as it has no specific goal or purpose. When you say "I plan on letting the Bard roll a Charisma (Persuasion, or whatever) check with disadvantage, because of the loss of nuance in translation," the vagueness of 'whatever' is likely founded in your lack of knowledge about what the party wants from the outcome, which is justified since the encounter hasn't happened yet. Will they try to convince the Lizardfolk that they just want to pass through the area and mean no harm? Persuasion. Will they try to connive the Lizardfolk into believing that they are allies, only to attack them later when their guard is down? Deception. Will they try to demonstrate to the Lizardfolk that they are the superior force, so that the Lizardfolk should back off? Intimidation. If the players just say 'we talk to the Lizardfolk', then you just roleplay the conversation without making any rolls. Only if they specify a desired outcome is a skill check called for, with the skill being appropriate to their stated goal.
Once you know what they are attempting, you can decide whether it is appropriate to give them disadvantage (or even advantage). As you say, "the loss of nuance in translation" might call for disadvantage in the first two cases, but if the Bard is simply threatening the Lizardfolk, that is perhaps a more 'universal language' that doesn't require translation.
For the remainder of this answer, let's assume that the party's goal will call for a Persuasion check.
Possibilities for resolving a check
(1) Suppose the Bard was working alone, and trying to Persuade the Lizardfolk of something abstract enough to require language. You could rule that they simply can't do it - no check allowed. The addition of the Wizard as translator makes the task possible, though at a disadvantage, because the bard is not fully capable of implementing their Charisma (Persuasion) when working through another. This would be similar to not allowing a skill check unless the character attempting it had an 'appropriate tool'.
(2) As SeriousBri explains, Intelligence checks are called for when attempting to communicate without using words. You could allow the Bard, acting alone, to attempt a flat Intelligence (Persuasion) check if you consider the idea simple enough to be communicated without words.
(3) As ValhallaGH says, the mechanic of "Working Together" exists. In this case, the Bard and Wizard could help one another (rather than the Bard simply using the Wizard as an imperfect tool). The requirements for this are (PHB 175):
A character can only provide help if the task is one that he or she could attempt alone. For example, trying to open a lock requires proficiency with thieves’ tools, so a character who lacks that proficiency can’t help another character in that task. Moreover, a character can help only when two or more individuals working together would actually be productive. Some tasks, such as threading a needle, are no easier with help.
In this case, it is up to the players to explain to you why each character could attempt this alone, and one could also assist the other in relevant ways. For example, either of these characters could attempt an Intelligence (Persuasion) check to communicate their peaceful intentions without words. If the Bard was making such a check, the Wizard could grant advantage by interjecting a few appropriate words in Draconic here and there. If the Wizard was making the check, the Bard could coach them on posture, carriage, appropriate gestures, etc., or supply them while the Wizard was communicating. Neither of these base checks are likely to be good (the Bard likely lacks a high Int mod, and the Wizard probably is not proficient in Persuasion), but working together they can at least have Advantage on what is a poor check for one of them.
Since they speak Draconic, the Wizard could attempt a Charisma (Persuasion) check alone, albeit not a great one. You might be tempted to allow the Bard to help them, granting Advantage on the Wizard's check, since the Bard can provide them with just the right words, tone, etc. However, keep in mind the requirement that both characters need to be able to make the check on their own in order to use the working together mechanic. If you have already ruled that the Bard cannot be allowed a Charisma (Persuasion) check by themselves (even at Disadvantage), then they cannot assist the Wizard with such a check. Similarly, the Wizard could not prepare a translation of the Bard's planned speech and hand it off for the Bard to try a Charisma (Persuasion) check working together, because that is not something the Bard could do alone.
A final note on Halitosis
There are lots of possible reasons, in-game, for a below average Charisma score - poor posture, lack of eye contact, speaks too softly, etc. If your game hasn't described why the Wizard has a Cha of 8, they just have a -1 Mod for no specific reason. But if your game narrative has specifically established that the Wizard does actually have bad breath, and this is the canonical reason for their Charisma penalty, you might consider not applying the penalty in this particular case (treat them as having Cha 10). Lizardfolk are omnivores and likely have as much meat in their diet as they can get. One can imagine they don't brush, floss, or rinse. My personal experience in feeding bearded dragons suggests Lizardfolk breath might not be that pleasant, so they may simply not notice the Wizard's breath, or might not have any cultural stigma attached to bad breath. Heck, it might even be considered an important social cue where their status is in part assessed by what they most recently ate.