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.
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.