Measuring the % of pectin in a fibre after enzymatic treatment with pectinase
Note that I do not have professional experience in the textile industry!

Supposed that the stems have been (mechanically) treated, and the "bark" is removed, the ruthenium red method should work.

In Crystal-Structure of Ruthenium Red and Stereochemistry of its Pectic Stain by Clarence Sterling, Am. J. Bot. 1970, 57, 172-175, the specific binding of Ruthenium Red (RR, CAS-RN: 11103-72-3) along a pectin chain, that is, between a $\ce{COOH}$ of one galacturonic acid unit and the $\ce{OH}$ of the next, has been described.

In a more recent publication, Qualitative distinction of carboxyl group distributions in pectins with ruthenium red, published in Bot. Bull. Acad. Sin., 1999, 40, 115-119 (PDF), the method was applied to orange peel pectines of different origin. Here, the dye-pectin adducts were precipitated by addition of $\ce{CaCl2}$ and centrifugated. Then, the absorbtion of the supernatant solution and a stock solution of the dye at $\lambda = 534\,\mathrm{nm}$ were compared.

Consequently, it should be possible to take fibre samples, suspend them and detemine whether they decrease the absorption of RR (= still contain pectin).

Are you planning to bleach these fibres in a way recently discussed in another question? It might be interesting to figure out whether these conditions (alkaline hydroperoxide) are sufficent to (partly) degrade the pectin.