that's precisely how i have felt for Brahmos and future Brahmos-2. let the missiles be sub sonic in Indian space and pump up boosters for supersonic/hypersonic stage later on.
Maybe possible for current Supersonic Bramhos to keep it subsonic in Indian Air & then cruising it to supersonic speed afterwords. It'll' involve mammoth work though.
But I highly doubt same logic applies to a Hypersonic missile. Because basically you see the scramjet technology incorporated in hypersonic missile is very complex, rather critical.
In scramjet tech, the air intake is supersonic & the same supersonic airflow is required to be maintained throughout the engine. There is very very short time to mix the fuel on board since the higher velocity of the airflow.This is the main difficulty in realizing the hypersonic speed i.e. speed beyond 5.5 MACH. The air is forced inside, compression & heating is done along with fuel is combusted expanding the gas. Any small irregularity/error in the structural geometry of flying body will result in greatest drag possible.
The compression as well as the exhaust is SUPERSONIC. Depending on the fuel, the kinetic energy of the air and the potential combustion heat release will be equal at around Mach 6+. As the speed increases makes the control of the flow within the combustion chamber more difficult. More speed we achieve difficult it gets to maintain the body in air without destroying it.
However we obtain the so called "HYPERSONIC" speed in the mean time.
Now when you are talking about keeping the initial phase subsonic & further hypersonic stage, its a lot complicated & unnecessary if we can master the hypersonic ability.
Because if tomorrow India or even India+Russia succeed in this technology; forget MTCR, US & every other power will be lining up to buy it with blank cheque in briefcase.