Hi Lars, you ask some excellent questions and I'm sorry it has taken me so long to respond to them! First, it sounds like your sourdough starter is working quite well when you add it to a levain, so why not continue to use it in this way? There are many great sourdough recipes that call for using an overnight levain, so why not take advantage of them? It's true that a whole rye starter encourages the lactic acid bacteria (LAB) more than the yeast component, so this may be part of the reason you're seeing less of a rise, but if adding white flour to the levain is all it takes to get a good rise, then your sourdough starter is still working. Secondly, when it comes to making sourdough rye breads, you may just need to adjust your expectations. This is because rye flour doesn't develop gluten in the same way wheat flour does; any rye bread recipe with a significant percentage of rye flour is going to be quite dense. This is just the nature of rye flour and rye breads. That doesn't mean that you can't make excellent sourdough rye breads with your rye starter. You might want to try our Rye Levain Pumpernickel recipe or Jeffrey's Sourdough Rye Bread recipe, as examples of dense, but delicious rye bread recipes. Keep in mind that rye flour ferments faster than white flour, so often rye flour doesn't work well with extended fermentation, and you'll frequently see a little yeast added to sourdough rye bread recipes. 

I don't think you need worry about your starter being "bad," unless you're seeing mold or a pink or orange streak/tinge growing on it. I don't normally recommend using the discard during the early days of starter creation because your starter is busy weeding out the unhelpful bacteria (which can sometimes smell quite bad), but once your starter is rising predictably it should be fine to bake with it. And, yes, baking should kill off most bacteria anyway. 

I hope this helps! Let us know how it goes. 

Barb

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