Thermography is a useful imaging technique as it works well in poor visibility conditions. High-resolution thermal imaging sensors are usually expensive and this limits the general applicability of such imaging systems. Many thermal cameras are accompanied by a high-resolution visible-range camera, which can be used as a guide to super-resolve the low-resolution thermal images. However, the thermal and visible images form a stereo pair and the difference in their spectral range makes it very challenging to pixel-wise align the two images. The existing guided super-resolution (GSR) methods are based on aligned image pairs and hence are not appropriate for this task. In this paper, we attempt to remove the necessity of pixel-to-pixel alignment for GSR by proposing two models: the first one employs a correlation-based feature-alignment loss to reduce the misalignment in the feature-space itself and the second model includes a misalignment-map estimation block as a part of an end-to-end framework that adequately aligns the input images for performing guided super-resolution. We conduct multiple experiments to compare our methods with existing state-of-the-art single and guided super-resolution techniques and show that our models are better suited for the task of unaligned guided super-resolution from very low-resolution thermal images.