Your two problems are highly related. See perhaps Boyd and Vandenberghe Chapter 5 on Lagrangian duality.
Let $\mathcal{W} = \left\{ \mathbf{w}: \mathbf{w}_l \leq \mathbf{w} \leq \mathbf{w}_u \right\}$
Optimization 1:
\begin{equation}
\begin{array}{*2{>{\displaystyle}r}}
\mbox{minimize (over $\mathbf{w}$)} & \frac{1}{2} \mathbf{w}'\Sigma\mathbf{w} \\
\mbox{subject to} & \mathbf{w}'\boldsymbol{\mu} = r \\
& A \mathbf{w} = \mathbf{0} \\
& \mathbf{w} \in \mathcal{W}
\end{array}
\end{equation}
Let me define an optimization problem 2b (similar to your optimization problem 2) to more closely match Lagrangian duality.
Optimization 2b:
\begin{equation}
\begin{array}{*2{>{\displaystyle}r}}
\mbox{minimize (over $\mathbf{w}$)} & \frac{1}{2} \mathbf{w}'\Sigma\mathbf{w} + \lambda \left( \mathbf{w}'\boldsymbol{\mu} - r \right) + \mathbf{v}' A \mathbf{w} \\
\mbox{subject to} & \mathbf{w} \in \mathcal{W}
\end{array}
\end{equation}
Lagrangian duality
Problem 1 and problem 2b are highly related problems. Define the Lagragian function as:
$$ \mathcal{L}\left(\mathbf{w}, \lambda, \mathbf{v} \right) = \frac{1}{2} \mathbf{w}'\Sigma\mathbf{w} + \lambda \left( \mathbf{w}'\boldsymbol{\mu} - r \right) + \mathbf{v}' A \mathbf{w} $$
where scalar $\lambda$ and vector $\mathbf{v}$ are Lagrange multipliers.
Your optimization problem 1 is:
$$\min_{\mathbf{w} \in \mathcal{W}} \max_{\lambda, \mathbf{v}} \mathcal{L}(\mathbf{w}, \lambda, \mathbf{v}) $$.
Min-max interpretation: First you pick $\mathbf{w}$ (to minimize the objective), and then (after observing your choice) I get to pick penalties $\lambda$ and $\mathbf{v}$ to maximize the objective. If you violate the constraints, I can choose arbitrarily large penalties so the objective is $\infty$!
This is a convex problem. If furthermore the feasible set has a non-empty relative interior then Slater's condition holds and then the duality gap is zero. We then have:
$$\min_{\mathbf{w} \in \mathcal{W}} \max_{\lambda, \mathbf{v}} \mathcal{L}(\mathbf{w}, \lambda, \mathbf{v}) = \max_{\lambda, \mathbf{v}}\min_{\mathbf{w} \in \mathcal{W}} \mathcal{L}(\mathbf{w}, \lambda, \mathbf{v}) $$.
Interpretation: If the duality gap is zero (i.e. the saddle point property), then the order doesn't matter! The max of the min is the same as the min of the max. The primal problem (the left hand side) is the same as the dual problem (on the right hand side).
Define the Lagrangian dual function as:
$$ g(\lambda, \mathbf{v}) = \min_{w \in \mathcal{W}} \mathcal{L}(\mathbf{w}, \lambda, \mathbf{v}) $$
Note that the dual function is the value obtained from solving optimization problem 2b. The dual problem is known as:
$$ \max_{\lambda, \mathbf{v}} g(\lambda, \mathbf{v}) $$
Summary
Define the Lagrangian dual function $g(\lambda, \mathbf{v}$) as value obtained from solving optimization problem 2b. If Slater's condition holds, then your optimization problem 1 is equivalent to the dual problem $\max_{\lambda, \mathbf{v}} g( \lambda, \mathbf{v})$.
There exists a $\lambda^*$ and a $\mathbf{v}^*$ such that solving problem 2b gives the same answer as problem 1.
Perhaps the real issue (as I go into in the comments) is in carefully defining your problem. If constraints really are hard constraints, then you can't violate them period. End of story. Where you seem to be going though is that perhaps some of these constraints are more goals than requirements. What's the right penalty then for violating these soft constraints? I don't know?
References
Boyd, Stephen and Lieven Vandenberghe, Convex Optimization, 2004
Rockafellar, R. T., Conjugate Duality and Optimization, 1974