There's a lot to unpack here, so bear with me as I try to answer each question one by one...
Powdered extracts will colour your product, there's no doubt about that, but some of the good stuff botanical extracts offer are all about the colour.
Proanthocyanidins are colourless molecules also called oligoflavonoids, condensed polyphenols, or hydrolyzable tannins. They called the latter because they can be hydrolyzed (the molecule is split by water into different compounds) in an acidic environment to produce anthocyanidins, which are coloured. They play a role in the stabilization of collagen and maintenance of elastin in the skin. They are being studied as water retention reducers, and capillary protectors. They can help the body to produce histamine to prevent allergic reactions. And they can be powerful anti-oxidants - they are about 20 times more powerful than Vitamin C and 50 times more powerful than Vitamin E.
Carotenoids are strong anti-oxidants that connect with free radicals to quench them. They're comparable to Vitamin C in inhibiting lipid peroxidation, which is the degradation of lipids in our skin. They tend to be orange to deep orange, and you can find them in extracts as well as oils.
Thus, my answer to one part of your question is there's a lot of value in the colour of our botanical ingredients.
In my class yesterday, a lovely participant suggested that the brown tinge in of green tea extract in our facial gel wasn't brown, it was "amber". I really like that! Now I have to find a way of describing products made with grapeseed extract as something other than "bloody".
How to use powdered extracts without precipitation? Stay within the suggested usage rates and note how soluble each extract might be. If the suggested usage rate for green tea is 0.5% and the suggested usage rate for rosemary extract is 0.5%, maybe use 0.25% of each and see what happens over time. (I've used three powdered extracts at a time without problems, but it really will depend on the product and what else is in it.)
You can get all kinds of different liquid extracts at our suppliers with differing levels of colour. For instance, I've had almost clear liquid willow bark extract to very very brown versions. I know some suppliers put the colour of the ingredient in their write up, but if they don't and it's important to you, then ask.
What does it mean if they're uncoloured or very lightly coloured? It doesn't mean the extracts don't have awesome properties, it just means those things like proanthocyanins aren't in there any more.
When it comes to the issue of preservation, botanical ingredients are harder to preserve, so you always want something broad spectrum in there to ensure long term stability and safety. If this is an issue, consider using oil soluble extracts, which don't require preservation. You can find quite a few at your local supplier - green tea extract is pretty common, for instance.
I can't tell to how to run your business or what to tell your customers, I can only share my experiences, but when I'm teaching classes, I encourage people to embrace the colour as part of the awesome power of botanicals. Yeah, I recognize a slightly brown lotion or body wash may not be the most beautiful thing in the world, but knowing that colour is full of awesome things makes it easier to appreciate.
Big posts on using powdered extracts
Extracts section of the blog
If you want to learn more about extracts, check out the section of the blog or take a look at my new e-zine on botanical extracts (part one).