Alpha Centauri (GOG version) is using up nearly 100% cpu

There are two options:

1. Upon completion building the Network Node, activate the Alien Artifact and press Ctrl+H (Set Home City). The game will suggest using the Artifact. Note: this works even if the unit has no moves remaining (e.g., it was Held in a city and passed its move).
2. When the Alien Artifact activated, just step away from the city and step back into the city. Since usually, each city has at least one road around, the move will take only 2 * 1/3 of Artifact's moving capacity.

Also, SMAX (Alpha Centauri Alien Crossfire) automatically unholds Alien Artifacts in the city upon building the Network Node or starting building a special project. I'm not sure if the older SMAC works the same way.
Note: if unheld, the unit may have already skipped its move, but it still can do Ctrl+H; see above.

Although the internet has non-authoritative (opinion) answers to your question [see 'terraforming hints', here], the game user manual (starting at the 'ecological risks' section [on page 54]) reads as follows (my comments are in the [] brackets):

'...each technological enhancement constructed on any square in a base's production radius increases that base's ecological disruption. In general, the more complex an enhancement (i.e. the longer it takes to complete), the greater the damage it causes. Also, the higher a base's mineral production, the greater the chance of ecological disaster.'

'Your ecological damage ranking, as shown on your base screen [under the label 'eco damage'] gives a percentage chance on each turn that Planet will react to your disruptions in the form of uncontrolled fungus blooms that wipe out all existing enhancements in a given square, The new fungus also often spawns native life forms.'

'Ecological damage can be minimized (or even eliminated entirely) through social engineering ['green' is especially good for this] and secret projects (such as the Pholus Mutagen).'

So the although the user manual seems to imply that any change you make to a square [including drill to aquifer] will cause some ecological disruption, this is not always true. I have found that while building farms, mines, roads, and especially boreholes increases eco disruption, building forest or fungus in squares [non-technological terraforming] tends to decrease eco disruption and some terraforming, like 'drill to aquifer', or raise/lower/flatten terrain are more or less neutral to eco disruption.

In general, if you plant sufficient forest and fungus squares and don't have too high a mineral production in any given city, eco disruption is easily avoided, even if you do a lot of terraforming.