Transmeta failed because they couldn't deliver the cost/performance ratio that they'd promised to customers. Toshiba (it was Toshiba, not Sony) cancelled that laptop product because they couldn't rely on Transmeta delivering the CPUs for it. Intel didn't impede them, because Intel didn't have to - they messed up themselves.
Intel pretty much ignored Transmeta - at this time, it was capturing Apple's business from Motorola and IBM: getting the last remaining non-Intel PC maker on board was something that was much more valuable to Intel.
And in any case, Intel's bullying isn't Microsoft's. If the two companies were so joined at the hip as you imply, then Microsoft would not have supported AMD's 64-bit Opteron chips at their launch back in 2003, and Opteron competed with Intel much more directly than Transmeta did.