It was suggested on math.stackexchange.com that I try to ask this question here.
Consider a bounded linear operator $A : U \to V$ where $U$ is finite dimensional and where $V$ is a separable Hilbert space, or with large dimension such that $A$ cannot be stored explicitly, being instead available as an algorithm for computing $y \mapsto Ay$. Let $f \in V$ and consider the standard least-squares problem: Find $x \in U$ such that $\|Ax-f\|=\text{min}!$. We assume that inner products of columns of $A$, i.e., the matrix elements of $M = A^*A$, can be computed efficiently, and similarly $A^*f$ can be computed efficiently. However, we also assume that that $M = A^*A$ is ill-conditioned.
Are there efficient algorithms for the solution of this least-squares problem that avoids the ill-conditioning of $A$?
Additional details added in edit:
In my concrete example, $A$ is on the form $$ Ae_i = u_i \in V = L^2(\mathbb{R}^n),$$ with prescribed vectors $u_i$, and where $\{e_i\}$ is some orthornormal basis for $U$. The normal equations read $$ Mx = A^* f, \quad M = A^* A,$$ which takes the usual matrix form when we expand $x = \sum_i x_i e_i$, and introduce the matrix with elements $M_{ij} = \langle u_i,u_j\rangle_{L^2}$, and the vector $(A^*f)_i = \langle u_i, f \rangle_{L^2}$. Thus, the normal equation is easy to write down and solve if $M$ is not ill-conditioned. However, it turns out in practice to be. The LSQR algorithm mentioned in the comments does not seem viable here, as it requires an algorithm for $u \mapsto A^* u$.
To be even more concrete, in the $V = L^2(\mathbb{R})$ case, I have $n = 3K$ basis functions. The first $K$ basis functions are gaussian functions $u_i(x) = \exp(-\alpha_i(x-z_i)^2)$, with $\alpha_i,z_i\in\mathbb{C}$. The remaining $2K$ basis functions are the derivatives of $u_i$ with respect to the complex parameters. Moreover, $f\in L^2$ is a function for which I have an algorithm for computing $\langle u_i, f\rangle_{L^2}$, $1\leq i \leq 3K$. Note that inner products of any pair of gaussians and their derivatives are readily computed, so I also have an algorithm for $M = A^* A$.