Yes, as long as they can see the target (according to Rules as Intended)

Jeremy Crawford confirms that this is indeed the intended interpretation of the spell's effects on the Jan. 19, 2017 episode of Dragon Talk ("Wolfgang Baur on DMing for Girl Scouts"). Starting at 36:20, he says (transcription done by me):

There are spells that create exceptions to this rule about needing a path clear of obstruction. One cantrip [that breaks] this rule is sacred flame. Sacred flame is one of the low level spells that has this text: "The target gains no benefit from cover for this saving throw." [...] So, they're getting no benefit from cover [...] and that includes total cover. So sacred flame is one of the few spells that allows you to target somebody even if they're behind total cover. [...] You can be looking through the window in the tower and cast it on someone outside.

So, mechanically, this means that, as long as the caster can see the target, they can target them regardless of how much cover they have. Since total cover is a type of cover, it also is ignored by sacred flame.

For comparison, the normal rules for targeting dictate that if a spellcaster is behind a sheet of glass with no possible line of effect to the target, they cannot target them with a spell.

Narrative explanation

Jeremy Crawford continued on from the above provides some reasoning behind the spell and why it was written as it is. While not vital for a mechanical understanding of the spell (the above logic should be more than sufficient), it is interesting nonetheless.

The narrative reason for that, the reason I wrote it that way, is that sacred flame is coming down from above the person. The idea is the cleric is calling this divine energy down on the target and it is not actually shooting out from the cleric, it's coming down. [Which is an exception] and in the game the exceptional always beats the general.

Because we are exploring line of effect, it is important to note what, exactly, the effect is. If the effect of light, for example, is to create light centered on the object, the transparent container blocks that light since it blocks line of effect via full cover. If, on the other hand, it makes the object glow brightly enough to emit that light, the effect is constrained on the object itself and the light is a desirable side effect, kind of like setting things on fire with a fireball. In that case, the light wouldn't be blocked by glass any more than torchlight would. The key to distinguishing this in the spell is the word "sheds."

You touch one object that is no larger than 10 feet in any dimension. Until the spell ends, the object sheds bright light in a 20-foot radius and dim light for an additional 20 feet.

I've checked the PHB. The only objects that shed bright light are also the sources of that light, whether it be the flame from produce flame or that of a candle. Light, therefore, makes an object glow and the light it sheds will go right through glass.

Darkness makes a similar distinction:

If the point you choose is on an object you are holding or one that isn’t being worn or carried, the darkness emanates from the object and moves with it.

If you cast darkness on an object, the magical darkness is being emitted and will pass through glass, as counterintuitive as it sounds. If you cast the spell on an area, it would be blocked by glass.