I want to double check on this because it sounds legit but sketchy. If a player controls a stardust dragon and activates the seal of orichalcos, then can the player use stardust dragon's effect to negate the activation then the seal uses it's own effect to resist being destroyed? This way all the player's special summoned monsters are not destroyed and stardust dragon comes back with 3000 ATK points assuming the opponent didn't use a set MST or something.

Yes, he can use Stardust's effect to negate Seal of Orichalcos' effect to destroy all the Special Summoned monsters he controls, and Orichalcos will be able to protect itself from destruction.
The Stardust will come back with 3000 ATK unless it was Special Summoned by Starlight Road.

My first thought was that it negates Seal's activation, therefore Seal would not be able to protect itself, as it is not really on the field.

Gallows wrote:

My first thought was that it negates Seal's activation, therefore Seal would not be able to protect itself, as it is not really on the field.

It doesn't negate Seal's Activation. Seal Activates, then Stardust Dragon negates the trigger (not really trigger, but let's call it that) effect of Seal, which will attempt to destroy all the Special Summoned monsters they control.
Stardust can't negate the activation of the card iself because it doesn't destroy anything until after it's activated (hence the continuous effects all apply when Stardust attempts to destroy Orichalcos).

That makes sense. This sounds legit. I have to make a deck with that comb now.

for further tips regarding seal

http://yugioh.wikia.com/wiki/Card_Tips:The_Seal_of_Orichalcos

... Why post that?...

UPDATE:
The YGO Wikia sucks. Here's the ruling:

Reaper of the Cards wrote:

Ok, let's put an end to this thread, and the whole confusion altogether. If Stardust activates its effect trying to negate Seal's destruction ability, Seal will be destroyed and sent to the graveyard.

There is a card that looks similar to Seal, and functions similarly too, Ancient Forest.

"When you activate this card, change any Defense Position monster(s) to face-up Attack Position."

Now let's look at the OCG lore of Seal of Orichalcos:

"このカードの発動時に、自分フィールド上の特殊召喚されたモンスターを全て破壊する。"
"Upon activation of this card, destroy all monsters that were Special Summoned on your side of the field."

Moving on, Stardust's text is pretty clear in such cases.

"When a Spell, Trap, Spell/Trap effect, or Effect Monster's effect is activated that destroys a card(s) on the field: You can Tribute this card; negate the activation and destroy it."

Now according to what we saw above about Seal's text, and when it is in fact activating its effect, we can see that Stardust activates its negation effect chained to Seal's effect upon activation. It is NOT a trigger-like effect of Seal, that needs the actual field spell successfully resolved on the field to be activated. It is an effect that activates when Seal activates. Nowhere it is written on Seal that this is a trigger-like effect. Moreover, the order in which Seal's effects are placed on the card's text is irrelevant. Seal has to successfully resolve on the field to apply its continuous "I am not destroyed" effect, and this is to happen much later than its "When this card is activated: Destroy all Special Summoned monsters you control." effect.

An effect that would require Seal to have been successfully resolved on the field to be activated would not include in its text the phrase: "When this card is activated:".

I hope I was clear on this and that there are no more questions/grey spots about how this would go down. I will leave this open for some time so the OP can see it and comment. Once again, I'll leave this open for the OP. Everyone else have already put in their two cents and opinions have been formed and presented. No more need for that.