A non-averaged cross-entropy loss is coming soon. Until then you can write your own using log_softmax and advanced indexing.
In addition, though I don’t think it helps you here, nn.LSTM now has support for variable-length sequences without including padding, meaning that sequence model results will not be affected by the influence of padding tokens even with bidirectional RNNs. There are utility functions provided for creating the packed array data structure (~TF’s TensorArray) needed for this.