Yes, the Czar was already dead and the Soviets in power by the time of the armistice. Thats one of the reasons they weren't invited to Versaille. (another being that they had "surrendered" to Germany already in the Treaty of Brest-Litovsk (sp?)
While the Tsar is dead and there is a Soviet government in Moscow, the Russian Civil War was still in full swing at the time the Versailles Treaty was being written up. I would imagine at least part of the reason for the lack of Russian participation was the fact that the Allies would have to decide which Russians to invite. Inviting the Soviets while most of the Allies are helping to supply the White Army would hardly work, and the Whites are much too factionalized to agree on a single agenda for Versailles.
As Neroon said, how much Germany is willing to intervene in the Russian Civil War will largely depend on how drained the Germans are from World War I; after four long years of trench warfare the populace will hardly want to get involved in another war, especially intervening in another country's civil war. However even if the Germans have are fairly exhausted the Central Powers would probably at least provide the Whites with logistical support in the form of their large surplus of military hardware and supplies. The Whites might also be allowed staging grounds within Belarus and Ukraine; unlike the largely seaborne Allied intervention of OTL, the Central Powers have a large land border with Russia.
The fact that areas like Ukraine, Poland, and the Baltics are under the control of the Central Powers is probably going to have a major effect on the course of the war as well, given that this closes off some of the more important areas of fighting in OTL. The Basmachi Revolt in Central Asia would likely receive far more external support with the Ottoman Empire intact, possibly enough that the Soviets would be unable to hold the region. Assuming the Soviets do win this altered Russian Civil War, the White emigre movement would also likely be changed in some way.