The positions provided in Marble are realistic and correct:
Actually the top 100 satellites/spacecrafts _are_ "close" to the earth's surface: Take the ISS for example which orbits at a height of 380 kms above earth (which equals about 3% of the earth's diameter) . Same for the HST which travels at a height of about 550km around our shiny blue Marble.
Many of the bright satellites are just orbiting closely to the atmosphere which is just a very thin layer on top of the earth's surface.

For the geostationary orbit (like GPS satellites) the situation is different indeed. However those are not enabled in Marble by default. If you enable them (this might only be possible easily in the desktop version) you'll see that the GPS satellites are indeed rendered by Marble just like in the pictures you show: at a height of about 35800 km.

We verified the positions and altitudes for a few satellites (we had this verified even by people who do this satellite stuff professionally) and so far up to our knowledge the positions are correct (except for the rare case of very elliptic satellite orbits where there is a slight minor difference to the actual position). If you still think that you have found some bug regarding the position of a certain satellite please tell us the name of the satellite and the time for which you tested and we will check.