There is so much wrong with what you quoted!
First, collinearity is not the same as correlation and can involve more than two variables.
Second, there is nothing wrong with any of the equations, and regression doesn't assign "effect" only association. What's wrong is using regression from an observational study to infer causation, but the regression didn't do that. "The fault, dear researcher, lies not in our statistics programs but in ourselves."
Third, the "true $\beta_1$" is probably not 0. Even at a given temperature, there is probably a relationship between shorts wearing and ice cream eating. People who feel warm when it is 75 degrees F are going to be more likely to wear shorts and eat ice cream at that temperature.
Fourth, this is not a multivariate regression, but a multiple one. Multivariate regression is when you have more than one dependent variable.
Now, to your question: You can easily have control variables with no problematic collinearity. The independent variables do not have to be perfectly orthogonal to each other. You can use collinearity diagnostics to see if you do have problematic collinearity (I prefer condition indexes to VIF, but they are both OK) and there are various ways to deal with it if you do have it (e.g. ridge regression, partial least squares, principal component regression, etc.).