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Haven't played it yet, but my understanding is that the interface is through the buttons, analogue sticks and touch screen. This should run fine on the Lite.
On a tangent though, personally, I'd think hard before getting the Switch Lite, the main advantage is battery life but the costs to overcome the shortcomings should you decide you want to play multiplayer or play a game such as SMP, for instance, will wipe out your savings. But it's your money.
I've played it now, and yeah it runs great on handheld mode. I prefer it to docked due to being able to use the touchscreen; it makes it much easier than using the Joy Cons for everything. Other than not being able to dock and possibly charging (Civ 6 takes far more than one charge to play a game, so if you want to do a long haul session, then I'll have to be charged and I don't know how easy it is to play the Lite while it's charging, the standard Switchvis a pain). There's no need to detach the Joy Cons and docked mode isn't the best way to play it imo, so Lite should be fine.