The bar doesnt open untill you help the guys guarding the door, this will happen eventually.
The mole is important but you can get info from him dead or alive, alive is better to avoid failed missions, but in the grand scheme not all that important.
Artifacts all have positives and negatives. green should help red hurts, altough as pointed out above bleeding ones dont conform, which is a big i assume.
You can negate the negative effects of artifacts with armour/suits and other artifacts. Early artifacts are actually amond the best iv found. Meat Chunks are about the best i have found, although a lot more have specific values.