You're options

You can ask them what their bench/diagnostic charge is to this point, pay that and pick up your laptop. You can probably find a diagnostic utility for your hard drive from the manufacturer's web site (probably what the Geek Squad uses) and test the drive yourself. You can download the various free malware packages and run these yourself. That pop-up should be easy enough to resolve yourself. Tracking cookies and suspected tracking cookies aren't necessarily threats but they sound suspicious. One way to avoid these is use other than IE. Use FF and set it up to remove cookies upon exit or add trusted sites as you wish to keep those cookies that are useful for you...such as those that remember you as a registered user, your banking institution etc.
Yes, the unaware can be taken advantage of and can't prove one way or another that a vendor is being completely honest. "Caveat Emptor" ( buyer, beware) is nothing new.