In a nutshell: no, you cannot use your camera to accurately measure light transmission. The problem is with the way your ISO control works on a digital camera. ISO is not a generic "amplify signal by X amount"; it is designed as a compensation adjustment to match the exposure index of the equivalent film stock. Therefore ISO 100 with one lens is not the same as ISO 100 with another. The ISO setting is far more esoteric than most people realize.

Let's say you were shooting at ISO 3200 at f/1.4 and 1/100, and with this camera, anything above ISO 3200 looks really terrible. If a lens with terrible light transmission was shot at those settings, the ISO portion of the exposure would boost the signal amplification to match whatever it determines "ISO 3200" should be at, meaning you're introducing a ton of signal noise. If on the other hand you shot with a lens with great light transmission at the same settings, you'd will still have the same exposure, but it would look cleaner: this is due to lower signal amplification.

Even worse, although ISO is standardized, you can measure it in a number of different ways; this means light transmission values will vary across different sensors, and not in a linear fashion. And this is just the tip of the iceberg; ISO values are computed in a myriad of complex ways that take into account the sensor, the sensor size, the resulting brightness of the image, and all sorts of computational processing.

Instead of using a camera's imaging sensor to measure light transmission you need to use something designed to measure actual light reception, not gather light into an image.

Edited for clarity.