Well, I'm not quite sure about assumptions used in applied micro studies, I guess that depends very much on the particular study and application. It's certainly true that as soon as you actually try to apply the theory, problems of measurement and comparability hit you hard and bad and often lead to an extreme emphasis on monetary values.

However, the point I'm trying to make above relates to basic micro theory as presented in any run-of-the mill undergrad or basic post-grad course. In that "EC101" context, you can easily operationalise "altruism" in a classic utility-analysis framework where people behave as self-maximisers. The only thing you have to do is to say that some people derive utility from "altruism" or "moral behaviour" and hence prefer altruistic and moral choices, even if it hurts them in terms of e.g. money.

For instance, a typical simple post-grad micro exercise is the following:

"The preferences of a consumer are represented by the utility function u= x+y. The price of a unit of good x is 2, the price of a unit of good y is p, and the income of the consumer is M. Moreover, the consumer is given a lump-sum subsidy of that can only be used to purchase good y.

(a) Define the utility maximisation problem of the consumer.
(b) Suppose that p does not equal 2. Find the optimal amounts of x and y as functions of p, the subsidy and M."

Now this is all very abstract, but notice that in spite of the rhetoric ("purchase" etc.), the variables are not specified. You could say y is "hundreds of dollars" or you could specify it as "visits to the agent's sick grandmother". It's just stuff the agent derives utility from, and in theory you could find a representation of his utility function and indifference curves by observing how he actually choses between money and visits. Similarly, the units of prices and subsidy are not specified.

So...I concede that applications are difficult, but the underlying theory itself is not invalidated by the "altruism" criticism.