I have a guest player who is being a secretly evil plant inside the party causing trouble. He's a sorcerer who wants to use subtle spell metamagic to stop the party from delving into his master's old lair, and he has a custom ring item that works as a hands-free arcane focus. He and I agreed that he'd give me signals about what to cast and where, and I'd roll the damage and keep track of the lost sorcerer points.

So the party is sneaking past a sleeping giant and the sorcerer signals fireball on the party to wake the giant. After the battle, the cleric says her passive perception (which is pretty high, admittedly) should have let her see where the fireball originated from, pointing out that fireball is:

A bright streak flashes from your pointing finger to a point you choose within range

Now, I assume the pointing finger is part of the somatic components of fireball and thus not necessary with the Subtle Spell metamagic. And spells that obviously originate from the caster like cone attacks, it wouldn't be particularly possible to hide the location of the caster. But fireball's beam effect doesn't seem to be a mechanic of the spell, more just flavor text.

I addressed the problem in-game by rolling a sleight of hand check against the cleric's passive perception using the sorcerer's stats and managed to keep it hidden and "it happened so fast you saw it came from behind you but nothing else", but is that the right solution?

But the more I think about it, the more complicated it seems. Does it follow the stealth rules where any attack, even long distance arrows, immediately gives away the position of the attacker? Would a subtle Psychic Scream be traceable to the caster despite having no visible ties to the caster?

Unclear, but it doesn't disguise fireball by default

It is worth noting that the spell description is in addition and, more importantly, separate from material, verbal, and somatic components.

For example, the 2019 Sage Advice Compendium states, in regards to suggestion,

Verbal components are mystic words (PH, 203), not normal speech. The spell’s suggestion is an intelligible utterance that is separate from the verbal component. The command spell is the simplest example of this principle. The utterance of the verbal component is separate from, and precedes, any verbal utterance that would bring about the spell’s effect.

I use this evidence to conclude that in the case of fireball, the bright streak from your pointed feature is a required portion of the spell's effect, outside of the verbal and somatic components that the metamagic removes.

Casting a spell attack, notably, does automatically reveal you

On PHB 195, under Unseen Attackers and Targets:

If you are hidden - both unseen and unheard - when you make an attack, you give away your location when the attack hits or misses.

The section does not specify for spells with a save DC (or other effects), so the default would be that it doesn't reveal you.

Subtle Spell only covers somatic components, not other spell effects

By the wording of Subtle Spell:

When you cast a spell, you can spend 1 sorcery point to cast it without any somatic or verbal components.

If we look at the basic rules on Somatic Spellcasting Components, we're given:

Spellcasting gestures might include a forceful gesticulation or an intricate set of gestures. If a spell requires a somatic component, the caster must have free use of at least one hand to perform these gestures.

Somatic components are specific hand gesture requirements necessarily for all somatic spells. This is separate from gestures specified within the spell itself, which are more akin to being part of the effect of the spell. Subtle Spell means you don't need to do the intricate hand signs or verbal parts to cast it, but once cast the effect takes place, which includes "A bright streak flashes from your pointing finger to a point you choose within range".

How perceivable/traceable this is, however, is up to the DM and the situation. I'd rule similar to how you did in the example you gave since even if you rule the hand does nothing, the bright flashing streak isn't a somatic component, and it has to come from somewhere.