Numerous quantum algorithms require the use of quantum error correction to overcome the intrinsic unreliability of physical qubits. However, error correction imposes a unique performance bottleneck, known as T-complexity, that can make an implementation of an algorithm as a quantum program run more slowly than on idealized hardware. In this work, we identify that programming abstractions for control flow, such as the quantum if-statement, can introduce polynomial increases in the T-complexity of a program. If not mitigated, this slowdown can diminish the computational advantage of a quantum algorithm. To enable reasoning about the costs of control flow, we present a cost model, using which a developer can analyze the T-complexity of a program under quantum error correction and pinpoint the sources of slowdown. We also present a set of program-level optimizations, using which a developer can rewrite a program to reduce its T-complexity, predict the T-complexity of the optimized program using the cost model, and then compile it to an efficient circuit via a straightforward strategy. We implement the program-level optimizations in Spire, an extension of the Tower quantum compiler. Using a set of 11 benchmark programs that use control flow, we show that the cost model is accurate, and that Spire's optimizations recover programs that are asymptotically efficient, meaning their runtime T-complexity under error correction is equal to their time complexity on idealized hardware. Our results show that optimizing a program before it is compiled to a circuit can yield better results than compiling the program to an inefficient circuit and then invoking a quantum circuit optimizer found in prior work. For our benchmarks, only 2 of 8 existing circuit optimizers recover circuits with asymptotically efficient T-complexity. Compared to these 2 optimizers, Spire uses 54x to 2400x less compile time.