In short, the answer to your question is no, there are no pure "good guys" in Germinal by Emile Zola--but only if you define "good guys" a certain way. It is true that there are no really outstanding moral characters who do the right thing every time they have the opportunity; however, within this harsh environment, there are certainly people who maintain a kind of nobility.
For example, Etienne Lantier genuinely wants to help the miners improve their lot. He generally takes the moral high ground, even in the case of his feelings for Catherine Maheu; and he does his best, at least for a time. Of course, his efforts at reform fall short and people die (including an innocent baby), and he does act in his own self-interest at the end of the strike. Despite that, he is not unscathed and pays a price for his actions. To that extent, he is a fairly noble-minded character even though his actions could not all be characterized as good.
Catherine Meheu is also a noble character in this novel. In this harsh and rather animalistic world of mining, she is strong, willing to work, and loyal to a fault. In another environment, her morals would certainly be considered questionable; in this world, however, she is firm of purpose, determined, and willing to take a stand even against her own father.
The Gregoires might be considered noble because they do not act specifically against the miners; however, they delude themselves into thinking that miners should not be paid or treated any better because they are rather brutish people and would only spend their extra money on their vices. Paul Negrel might also be in this category, for he does attempt to be at least a bit humane to the miners; in the end, however, his interests lie with the mine and its owners.
While there are no clear-cut, undiluted "good guys" in the novel, there are certainly some characters who are absolutely and unequivocally "bad guys," such as the self-absorbed Cheval and the greedy and selfish Monsieur Hennebeau.
Unfortunately, Germinal is a novel which depicts a desperate and demoralized group of people stuck in a dark (literally and figuratively) and debilitating way of life. We should not be surprised, then, that they will fight over bits of bread or pennies or work. Zola says this:
They were brutes, no doubt, but brutes who could not read, and who were dying of hunger.
It is difficult to be noble or even good under such circumstances, but a few characters do manage to rise to nobility on occasion. It is not much good, but it is the only good there is in the harsh and unforgiving world of mining.