Why not blast the surface to glass?
Well, it all about the application of force in a measured and logical manner. You can bomb people fairly frequently and still have them pop their head up afterward to cause problems for you, so why make the ants madder by pounding them more then you need to or beyond what is cost effective for you. Also, in many cases you want to STAND on the ground and occupy it so making the surface uninhabitable would not help you much. Also, I would assume blasting the surface of someone's planet until it was molten glass would be a "sticking point" during the peace negotiations later.
When the Confederation invades the Skink home world here is what they should do.
1. 2 day orbital bombardment on major highways, supply depots, power supply, cities etc
2. 5 week raptor air strikes on skink troops
3. Force Recon goes in for 3 weeks and sets up bases with air support
4. Marines come followed by army
5. Take Capital
6. Force the Skink emperor to sign a treaty
7. Peace treaty is signed end of the war.
You make it sound soo easy man! The skinks can probably hide from the bombardment and use AA against the raptor. The only thing that Confederation can do is gather more intel on the enemy and improve relationship with other planets to make a coalition. Intercept the Skinks from invading other planets. I doubt the Skinks want to sign a peace treaty, they most likely want to destroy humanity.