Is upaya a lie?

His upaya wasn't a deception, not evil, and definitely not a lie. Say, one takes up Taekwondo, Judo, and Karate. Are they 3 different vehicles? yes (meaning there're different forms, methods, and techniques). Are they one vehicle? yes (meaning the ultimate goal is the same, maximizing one's survivability in combat and perfecting one's character).

"The “Expedient Means” (second) chapter of the Lotus Sutra says, “The Buddhas, utilizing the power of expedient means, apply distinctions to the one Buddha vehicle and preach as though it were three.” It also says, “In the Buddha lands of the ten directions there is only the Law of the one vehicle, there are not two, there are not three.”

Nichiren Buddhism Dictionary

It's a question of tailoring the teaching to be most useful to the person given their stage of realisation. Thus in Mahayana there are the 'Three Turnings of the Wheel' - each suitable at their level. But it's all one process and one teaching.

Ted Wrigley's answer is the right one in my opinion, and I will just quote an example here.

One person may still have self view and is therefore within the ignorance bubble or "world" of self view.

In SN 44.10, Vacchagotta, who had deeply entrenched self view and who was then incapable of understanding dependent origination or anatta, asked the Buddha whether there is a self or there isn't a self.

The Buddha did not want to mislead him by saying there is a self (i.e. eternalism), and also did not want to confuse him by saying there isn't a self (i.e. annihilationism). The Buddha could also see that Vacchagotta was not capable of understanding dependent origination and anatta at that point in time. So, he just kept silent.

For such persons, the Buddha employed skillful means (upaya) by teaching reflections such as the one below so that they may abandon the habit of misconduct and cultivate virtue.

This is skillful means because thinking "I am", associating self with the five aggregates and pondering a future state of self (such as rebirth), is based on conceit and also self view. However, the Buddha still employed it in a skillful way, despite it being inconsistent with the higher practice associated with anatta.

Telling lies to mislead others for malevolent reasons or for personal gain is just like injuring others with a knife. However, in this case, the Buddha is using the "knife" like a skillful surgeon to remove the tumour of misconduct. This is teaching the right view with effluents according to MN 117.

“And for the sake of what benefit should a woman or a man, a householder or one gone forth, often reflect thus: ‘I am the owner of my kamma, the heir of my kamma; I have kamma as my origin, kamma as my relative, kamma as my resort; I will be the heir of whatever kamma, good or bad, that I do’? People engage in misconduct by body, speech, and mind. But when one often reflects upon this theme, such misconduct is either completely abandoned or diminished. It is for the sake of this benefit that a woman or a man, a householder or one gone forth, should often reflect thus: ‘I am the owner of my kamma, the heir of my kamma; I have kamma as my origin, kamma as my relative, kamma as my resort; I will be the heir of whatever kamma, good or bad, that I do.’
AN 5.57

Meanwhile, for a more advanced practitioner like Bahiya, the Buddha taught anatta. This is teaching the noble right view according to MN 117.

"Then, Bāhiya, you should train yourself thus: In reference to the seen, there will be only the seen. In reference to the heard, only the heard. In reference to the sensed, only the sensed. In reference to the cognized, only the cognized. That is how you should train yourself. When for you there will be only the seen in reference to the seen, only the heard in reference to the heard, only the sensed in reference to the sensed, only the cognized in reference to the cognized, then, Bāhiya, there is no you in connection with that. When there is no you in connection with that, there is no you there. When there is no you there, you are neither here nor yonder nor between the two. This, just this, is the end of stress (suffering)."
Ud 1.10

The starting point of Buddhism is the idea that everyone begins in a state of ignorance. It is our ignorance that creates tanhā and dukkha, and it is the cessation of tanhā and dukkha that brings about wisdom and enlightenment. But ignorance, by its nature, comes in a multitude of forms. Your ignorance is not the same as my ignorance, his ignorance is not the same as hers, theirs is not the same as ours...

Upaya is an acknowledgement that we are all working out of different bubbles of ignorance, and that — so long as we are trapped in our own bubble — different tools might be 'skillful' for the context of ignorance we happen to be trapped in. Even tools that are not entirely correct might be sufficient for the state we are in. For instance, someone deeply attached the sensual world, filled with urges and cravings and jealousies, might find a more structured, disciplined environment useful (sravakayana); someone more critical and mind-oriented might find it hard to accept and embrace doctrine, and might find an independent path useful (pratyekabuddhayana).

There's no value judgement to this; it makes no sense to think that your ignorance is right and my ignorance is wrong. And we don't want to commit to a one-size-fits-all policy that helps some more than others. In that sense, upaya is a form of compassion, because it allows for the differences in our misunderstandings so that all can see progress.