The upper end of tornadoes can do an amazing amount of damage, and your character can place an EF5 tornado where ever they want it. Unfortunately though the Great Pyramid of Giza is a formidable opponent. It will definitely take damage from the tornado, but it will still be standing afterwards.
It was hard to determine if wind could lift a limestone block until I found an article about a tornado from 1990:
In June of 1990, an exceptionally violent tornado formed in the desert-land of southwest Texas. Near the end of the tornado’s path in Bakersfield Valley, a production facility was destroyed (at left) and three oil tanks weighing 180,000lbs were moved three miles to the east. Two of the tanks were found 600ft up a hillside with a 40 degree incline. This is one of the most impresive instances of tornado damage ever recorded and perhaps the only documented instance of an object over 100,000 lbs being moved a long distance.
Limestone weighs 2611 kg/cu.m. Doing some basic math each limestone block would weigh roughly around 3,088 kg. Note that some of the lower blocks in the pyramid are much bigger and can weigh five times that amount. If a tornado can push something weighing over 80,000 kg uphill then a tornado being directly manipulated by a person should be able to dislodge and push limestone blocks off the pyramid.
How long to destroy the pyramid
Given enough time a tornado could turn the Great Pyramid of Giza into a pile of rubble, but the question then becomes how long will it take to do it. Unfortunately there is a time limit. Your character will likely not have more than an hour to pull this off. After an hour the tornado will want to dissipate on its own or by that point your character will have to flee from the angry locals.
It has been estimated that the pyramid has 2.3 million blocks. If your character can take off even the top half of the pyramid, and leave the bottom half in a mess, then the mission is accomplished. The top half the pyramid only makes up ~12% of the total volume of the pyramid. So in order to remove that top half your tornado will need to remove approximately 276,000 stones in one hour or 76.7 stones a second. Needless to say I doubt the amount of stone removed will come close to that rate.
Where to form the tornado
For now lets table the time problem and look at where to perform the deed. The Great Pyramid at Giza is a tourist attraction and so is surrounded by security. If you were to even attempt to form some kind of weather event there you will likely end up shot. So you will need to form your tornado in a place which will not draw too much attention and that you can get it to your intended destination. Looking at Google maps of the area around the pyramid the only vector that you have available that will not go over populated areas is come up from the south:
Take an off road vehicle onto the Ring Rd. - Cairo--Alafayoom Rd, go off road for a bit, and then take your time to whip up your tornado there. Once it is ready send in north, and park the tornado on the Great Pyramid. By doing this you will also likely destroy/damage the Quarry of Menkaure and the Great Sphinx of Giza.
A single normal weather phenomena will not be enough to destroy the Great Pyramid of Giza. However, if you park the tornado between it, the Quarry of Menkaure and the Great Sphinx of Giza, and make the tornado the right size even if you do not fully destroy any of them, the overall damage should get your message across.