Sadly, this article has been authored by a thoroughly ignorant person.

During the Hamod-ur-Rehman Commission, General Niazi (the general who shamelessly surrendered with 90,000 troops under his command) himself admitted that there were some cases of rape and that he was powerless to stop the killing, arson and rapes. (Source: page 13 of the Report).

As for the killings, here's another snippet from the report:

Maj. Gen. Nazar Hussain Shah, GOC 16 Division, conceded that "there were rumours that Bengalis were disposed of without trial." Similarly, Brigadier Abdul Qadir Khan (Witness No. 243) Commander 93 (A)? admitted that "a number of instance of picking up Bengalis did take place." Lt. Col. S. S. H.
Bokhari, CO of 29 Cavalry, appearing as Witness no 244, stated that "In Rangpur two officers and 30 men were disposed of without trial. It may have happened in other stations as well." An admission was also made by Lt. Col. S. M. Naeem (Witness No 258) CO of 39 Baluch that "innocent people were killed by us during sweep operations and it created estrangement amongst the public."

Here's a link to a full version of the report.