LTV is clearly normative, and it's why people still try to revive it. The idea that factory owners are exploiting their workers has a certain intuitive appeal as a moral proposition.

The LTV wasn't exactly thrown out -- there are situations where marginalism and the LTV exactly coincide -- but it was superseded because outside a narrow sphere it becomes incoherent. The classic example is technological substitution -- if you have two ways of making something, one that is capital-intensive and one that is labor-intensive, then you will probably pick the one that's cheaper. So you can't calculate the labor content of a good independently of prices.

The specific issues you enumerate are issues within Marxist economics in general. The LTV was superseded well before Samuelson's paper on the transformation problem.