I have to concede your point about MSF (I thought I'd seen a reference for them, but can't now find it). As for the others, I think the allegations weigh heavily against Gaddafi's forces. Here's a sampling:
Libyan paramedics targeted by pro-Gaddafi forcesTwo medics from the Libyan Red Crescent trying to retrieve a body near the town of Misratah were injured by shooting from a nearby military installation belonging to the Hamza Brigade, a military force loyal to Colonel al-Gaddafi.
"This was a deliberate attack on medical professionals, who were wearing full medical uniform and arrived in two clearly marked Red Crescent ambulances," said Malcolm Smart, Amnesty International's Middle East and North Africa director.
Libya: Governments Should Demand End to Unlawful KillingsThe African Union and African, Western, and Arab countries that have relations with Libya should urge the Libyan government to stop the unlawful killing of protesters, Human Rights Watch said today. In the last three days, the death toll of protesters reported to Human Rights Watch by hospital staff and other sources has reached at least 173.
Accounts of the use of live ammunition by security forces, including machine gun fire, against protesters near the Katiba in Benghazi on February 19, 2011, resulting in dozens of deaths and injuries, raise serious concern that the authorities are using unjustified and unlawful force.
From:
http://www.hrw.org/en/news/2011/04/17/libya-indiscriminate-attacks-kill-civilians">Libya: Indiscriminate Attacks Kill Civilians
"Libyan government forces have repeatedly fired mortars and Grad rockets into residential neighborhoods in Misrata, causing civilian casualties," said Peter Bouckaert, emergencies director at Human Rights Watch. "The Soviet-made Grad in particular is one of the world's most inaccurate rocket systems and should never be fired in areas with civilians."
These indiscriminate attacks come alongside the use by Libyan government forces of cluster munitions in civilian-populated areas of Misrata, documented by Human Rights Watch on April 15.
Libya has 60 days to respond to an application alleging serious and widespread violations of the African Charter, including the repression of peaceful demonstrations and the use of heavy weapons and machine guns against its populationBased on evidence collected by our organizations, the ACHPR filed an application to the African Court against Libya alleging “serious and widespread” violations of various articles of the African Charter on Human and Peoples’ Rights, ratified by Libya in 1986. The allegations made against Libya include the repression by Libyan security forces of peaceful demonstration in February 2011, the excessive use of heavy weapons and machine guns against the population and the massive arrest and detention of demonstrators.
From:
Libya: Strategy of scorched earth, desire for widespread and systematic eliminationGaddafi is implementing a strategy of scorched earth. It is reasonable to fear that he has, in fact, decided to largely eliminate, wherever he still can, Libyan citizens who stood up against his regime and furthermore, to systematically and indiscriminately repress civilians. These acts can be characterised as crimes against humanity, as defined in Article 7 of the Rome Statute of the International Criminal Court.