Jason, I just ran mine externally in a bucket and changed the water every 5 minutes or so for about 20 mins until the water ran clear even on startup.... I don't think that stuff will harm your tank, but it sure couldn't look great! 
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135G Mixed Reef. Bullet 2, 25 gal refugium, 2 X250W MH + 4X 96W PC\'s, DIY Calcium Reactor, Coralife 1/6 HP Chiller, Phosban, Tunze, 2 closed loops & SQWD\'s, Seios, Coralife 4 stage RO/DI & a bunch of other expensive gadgets... I may never retire, but I'm gonnahavahelluvanaquarium!
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