When standing before certain men the philosopher regrets that thinkers are but perishable tissue, the artist that perishable tissue has to think. Thus to deplore, each from his point of view, the mutually destructive interdependence of spirit and flesh would have been instinctive with these in critically observing Yeobright.
This could be expanded to the following:
When standing before certain men, the philosopher regrets that thinkers are just perishable tissue, and the artist regrets that perishable tissue has to think. Therefore, when critically observing Yeobright, both the philosopher and the artist would instinctively deplore the mutually destructive interdependence of spirit and flesh, although they would deplore it from different points of view.
Answers to the questions in the body.
Who is he referring to when he says "with these"?
"These" are the philosopher and the artist.
What does he mean by "the artist that perishable tissue has to think"?
Why does the artist regret that perishable tissue has to think?
The surrounding context helps to answer these questions. The preceding paragraph says "He already showed that thought is a disease of flesh, and indirectly bore evidence that ideal physical beauty is incompatible with emotional development and a full recognition of the coil of things. Mental luminousness must be fed with the oil of life, even though there is already a physical need for it; and the pitiful sight of two demands on one supply was just showing itself here."
This is saying that mental development has a negative effect on the body and competes with it for resources ("the oil of life"). An artist, who presumably would appreciate physical beauty above all else, would regret that Clym Yeobright's physical appearance had been negatively affected by his thoughts, and would prefer that all of the "oil of life" had been left to feed his flesh.