Exod. 12:9 commands the Israelites: "Do not eat any of it [the Passover lamb sacrifice] raw, or boiled/cooked [bsl] in any way with water, but rather roasted over fire, its head with its legs and entrails". Deut 16:7, however, requires that "you shall boil/cook [bsl] it and eat it in the place where the Lord your God shall choose". One attempts to reconcile the two evidently incompatible verses is to translate bsl in the second verse as 'roast'. Nonetheless, this ignores the fact that however the verb is translated, one verse prohibits performing the action (of bissul) while the other requires it. (From the Article "Clearing Peshat and Derash by Stephan Garfinkel published in Hebrew Bible Old Testament: The History of Its Interpretation,I/2: The Middle Ages page 130.)
No, I'm afraid that you are ignoring the fact that Exodus 12:9 does not make an unqualified prohibition against bishul, only bishul in water. The two verses are simply not mutually exclusive. Indeed the verses need to clarify that bishul is prohibited if it is done "with water" implies that there is such a thing as bishul without water.